diff --git a/bioinfoconda/docker/Dockerfile b/bioinfoconda/docker/Dockerfile
deleted file mode 100644
index 74eb346..0000000
--- a/bioinfoconda/docker/Dockerfile
+++ /dev/null
@@ -1,64 +0,0 @@
-FROM ubuntu:18.04
-
-# Set the default shell
-SHELL ["/bin/bash", "-c"]
-
-# Add the docker:bioinfo user
-RUN addgroup --gid 5000 bioinfo \
-    && yes | adduser --quiet --disabled-password \
-	--no-create-home --gid 5000 docker
-
-# Install base system utils
-RUN apt-get update && apt-get install -y \
-        gawk \
-	git \
-        locales \
-        python \
-        wget \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set the locale
-RUN locale-gen en_US.UTF-8 \
-    && update-locale LANG="en_US.UTF-8" \
-    && update-locale LANGUAGE="en_US.UTF-8"
-
-# Replicate xavier's directory structure in the image
-RUN mkdir -p /bioinfo/bioinfotree \
-        /bioinfo/data \
-        /bioinfo/prj
-
-# Add bioinfotree tools
-COPY bioinfotree /bioinfo/bioinfotree
-
-# Install miniconda3
-RUN wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /bioinfo/Miniconda3-latest-Linux-x86_64.sh \
-    && bash /bioinfo/Miniconda3-latest-Linux-x86_64.sh -b -p /bioinfo/miniconda3 \
-    && rm /bioinfo/Miniconda3-latest-Linux-x86_64.sh
-
-# Set permissions
-RUN chown -R docker:bioinfo /bioinfo \
-    && chmod -R 2775 /bioinfo
-
-# Add bioinfotree's and miniconda's executables to $PATH
-ENV PATH="/bioinfo/bioinfotree/local/bin:/bioinfo/miniconda3/bin:$PATH" \
-    PYTOHNPATH="/bioinfo/bioinfotree/local/lib/python" \
-    PERL5LIB="/bioinfo/bioinfotree/local/lib/perl" \
-    LC_ALL="en_US.UTF8" \
-    BIOINFO_ROOT="/bioinfo"
-
-# NOTES ON OCCAM
-#
-# On occam, when we run an image the user is emariell:emariell. When whe 
-# build the image, the user is root (or the one specified with the 
-# "USER" directive in the dockerfile). The umask cannot be set (unless 
-# we set it with a script), so the new files created under /bioinfo will 
-# not be writable by the group. Given all this, I think that the most 
-# economic option is to chmod 777 everything.
-# 
-# Setting the workdir does not work on occam, either. We have to 
-# manually cd into the required directory.
-#
-# PYTHONPATH and PERL5LIB must be reset in the project dockerfile to 
-# include the bioinfotree libraries. Appending the old variables does 
-# not work, but maybe there is a right way to append variables for 
-# dockerfiles. I should investigate about that.
diff --git a/bioinfoconda/docker/dockerignore b/bioinfoconda/docker/dockerignore
deleted file mode 100644
index 8b37f4d..0000000
--- a/bioinfoconda/docker/dockerignore
+++ /dev/null
@@ -1,4 +0,0 @@
-data
-docker
-miniconda3
-prj
diff --git a/bioinfoconda/local/bin/X-conda b/bioinfoconda/local/bin/X-conda
deleted file mode 120000
index c7dc556..0000000
--- a/bioinfoconda/local/bin/X-conda
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-conda.sh
\ No newline at end of file
diff --git a/bioinfoconda/local/bin/X-conda-export b/bioinfoconda/local/bin/X-conda-export
deleted file mode 120000
index 7c990ab..0000000
--- a/bioinfoconda/local/bin/X-conda-export
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-conda-export.sh
\ No newline at end of file
diff --git a/bioinfoconda/local/bin/X-conda-get-channels b/bioinfoconda/local/bin/X-conda-get-channels
deleted file mode 120000
index a215fec..0000000
--- a/bioinfoconda/local/bin/X-conda-get-channels
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-conda-get-channels.pl
\ No newline at end of file
diff --git a/bioinfoconda/local/bin/X-conda-get-specs b/bioinfoconda/local/bin/X-conda-get-specs
deleted file mode 120000
index c9ec4c8..0000000
--- a/bioinfoconda/local/bin/X-conda-get-specs
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-conda-get-specs.pl
\ No newline at end of file
diff --git a/bioinfoconda/local/bin/X-conda-install b/bioinfoconda/local/bin/X-conda-install
deleted file mode 120000
index e1746d6..0000000
--- a/bioinfoconda/local/bin/X-conda-install
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-conda-install.sh
\ No newline at end of file
diff --git a/bioinfoconda/local/bin/X-getdata b/bioinfoconda/local/bin/X-getdata
deleted file mode 120000
index ffe9e1a..0000000
--- a/bioinfoconda/local/bin/X-getdata
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-getdata.pl
\ No newline at end of file
diff --git a/bioinfoconda/local/bin/X-mkprj b/bioinfoconda/local/bin/X-mkprj
deleted file mode 120000
index d2389ba..0000000
--- a/bioinfoconda/local/bin/X-mkprj
+++ /dev/null
@@ -1 +0,0 @@
-../src/X-mkprj.sh
\ No newline at end of file
diff --git a/bioinfoconda/local/lib/bash/bash_completion b/bioinfoconda/local/lib/bash/bash_completion
deleted file mode 100644
index 0d0e734..0000000
--- a/bioinfoconda/local/lib/bash/bash_completion
+++ /dev/null
@@ -1,33 +0,0 @@
-#######
-# cdp #
-#######
-
-# FIXME: prjhome does not change; we should not define it locally inside 
-# the _cdp function.
-
-function _cdp
-{
-        local cur=${COMP_WORDS[COMP_CWORD]}
-        local prjhome="$BIOINFO_ROOT/prj"
-        local IFS=$' \t\n'
-
-        IFS=$'\n'
-        COMPREPLY=( $(cd $prjhome && compgen -d -- "$cur") )
-        COMPREPLY=( "${COMPREPLY[@]/%//}" )
-        IFS=$' \t\n'
-
-        # variable names if appropriate shell option set and no 
-        # completions
-        if shopt -q cdable_vars && [[ ${#COMPREPLY[@]} -eq 0 ]]; then
-                COMPREPLY=( $(compgen -v -- "$cur") )
-        fi
-
-        return 0
-}
-complete -o filenames -o nospace -o bashdefault -F _cdp cdp
-
-#############
-# snakemake #
-#############
-
-complete -o filenames -o nospace -o bashdefault -C snakemake-bash-completion snakemake
diff --git a/bioinfoconda/local/lib/bash/bash_functions b/bioinfoconda/local/lib/bash/bash_functions
deleted file mode 100644
index 193ca32..0000000
--- a/bioinfoconda/local/lib/bash/bash_functions
+++ /dev/null
@@ -1,85 +0,0 @@
-#####################
-# Logging Functions #
-#####################
-
-# FIXME: perhaps warn and info should not print to stderr.
-
-# Input: error string
-function bug()
-{
-	>&2 echo "BUG: $1"
-	exit 99
-}
-
-# Input: error string, exit code
-function error()
-{
-	>&2 echo "ERROR: $1"
-
-	re='^[0-9]+$'
-	if ! [[ $2 =~ $re ]] ; then
-		bug "argument to error() is not a number."
-	else
-		exit $2
-	fi
-}
-
-# Input: warning string
-function warn()
-{
-	>&2 echo "WARNING: $1"
-}
-
-# Input: info string
-function info()
-{
-	>&2 echo "INFO: $1"
-}
-
-###############################
-# Path Manipulation Functions #
-###############################
-
-# NOTE: By "Output" we mean what is sent to the standard output; the 
-# return value is 0 if no error occurred, different from 0 otherwise.
-
-# Input: an absolute path
-# Output: the project contained in that path, if any
-function extract_prj
-{
-        if [[ $1 != "${BIOINFO_ROOT}/prj"* ]]; then
-                return 1
-        fi
-
-        if [ "$1" == "$BIOINFO_ROOT/prj" ]; then
-                echo $BIOINFO_ROOT/prj
-        else
-                echo $1 | cut -d '/' -f 4
-        fi
-
-        return 0
-}
-
-# Input: a relative path
-# Output: the absolute path
-function absolutise
-{
-        if [[ $1 == "/"* ]]; then
-                echo $1
-                return 0
-        fi
-
-        abs_path=$PWD
-        rel_path=`echo $1 | sed 's#^./##'`
-
-        for d in `echo $rel_path | cut -d '/' -f 1- --output-delimiter=' '`; do
-                if [ "$d" == ".." ]; then
-                        abs_path=`dirname $abs_path`
-                else
-                        abs_path=$abs_path"/"$d
-                fi
-        done
-
-        echo $abs_path
-        return 0
-}
diff --git a/bioinfoconda/local/lib/bash/bash_utils b/bioinfoconda/local/lib/bash/bash_utils
deleted file mode 100644
index bf20230..0000000
--- a/bioinfoconda/local/lib/bash/bash_utils
+++ /dev/null
@@ -1,73 +0,0 @@
-source $BIOINFO_ROOT/bioinfoconda/local/lib/bash/bash_functions
-
-#######
-# cdp #
-#######
-
-export BIOINFOCONDA_OLDPWD="${BIOINFO_ROOT}/prj"
-
-# Update BIOINFOCONDA_OLWPWD
-function cd
-{
-        # Find current project, if any
-        cur_prj=""
-        if extract_prj $PWD > /dev/null; then
-                cur_prj=`extract_prj $PWD`
-        fi
-
-        # Find new project (exclude cd options), if any
-        new_prj=""
-        for p in $*; do
-                if [[ $p != "-"* ]] && extract_prj $(absolutise $p) > /dev/null; then
-                        dest=$p
-                        new_prj=`extract_prj $(absolutise $dest)`
-                fi
-        done
-
-        # If we are entering another project...
-        if [ "$new_prj" != "" ]; then
-                # ...From another project
-                if [ "$cur_prj" != "" ] && [ $cur_prj != $new_prj ]; then
-                        BIOINFOCONDA_OLDPWD=$PWD
-                fi
-		# Elif we go out to the outside world...
-        elif [ "$new_prj" == "" ]; then
-                # ...From a project
-                if [ "$cur_prj" != "" ]; then
-                        BIOINFOCONDA_OLDPWD=$PWD
-                fi
-        fi
-
-        builtin cd "$@"
-        return $?
-}
-
-# Note that in cdp we use the cd function we defined above, therefore we 
-# need not worry about updating BIOINFOCONDA_OLDPWD
-function cdp
-{
-        prj_root=${BIOINFO_ROOT}/prj
-
-        if [ "$#" == "0" ]; then
-                cd $prj_root
-        elif [ "$#" == "1" ]; then
-                if [ $1 == "-" ]; then
-                        cd $BIOINFOCONDA_OLDPWD
-				elif [ $1 == "." ]; then
-						if extract_prj $PWD > /dev/null; then
-								cur_prj=`extract_prj $PWD`
-								cd $prj_root/$cur_prj/dataset
-						else
-								cd $prj_root
-						fi
-                else
-                        cd $prj_root/$1
-                fi
-        else
-                echo "ERROR: Too many arguments."
-                echo "Usage: cdp [prjname]"
-                return 1
-        fi
-
-        return $?
-}
diff --git a/bioinfoconda/local/src/X-conda-export.sh b/bioinfoconda/local/src/X-conda-export.sh
deleted file mode 100755
index 2a6c4fe..0000000
--- a/bioinfoconda/local/src/X-conda-export.sh
+++ /dev/null
@@ -1,63 +0,0 @@
-#!/bin/bash
-
-source $BIOINFO_ROOT/bioinfoconda/local/lib/bash/bash_functions
-
-# Usage string
-read -r -d '' usage << END
-Usage:
-	X-conda export
-
-Options:
-	-h		Prints this help
-
-Notes:
-	The environment is exported in the local/condafiles of the project
-	and the files are ordered by name and exportation date.
-
-Reporting bugs:
-	federicomarotta AT mail DOT com
-END
-
-# Validate environment and define defaults
-if [[ -z "${CONDA_PREFIX}" ]]; then
-        error 'You must be inside a conda environment' 3
-fi
-
-options=h
-longoptions=help
-
-date=$(date +%Y-%m-%d)
-prjname=$(basename ${CONDA_PREFIX})
-prjpath=${BIOINFO_ROOT}/prj/$prjname
-env_file=$prjpath/local/condafiles/${prjname}_${date}.yml
-
-# Parse the options
-PARSER=$(getopt --options=$options --longoptions=$longoptions --name "$0" -- "$@")
-eval set -- "$PARSER"
-
-while true; do
-	case "$1" in
-		-h|--help )
-			echo "$usage"
-			exit 0
-			;;
-                -- )
-			shift
-			break
-			;;
-		* )
-			error "Unexpected arguments. $usage" 3
-			shift
-			;;
-	esac
-done
-
-# Start the real script
-info "Exporting environment..."
-conda env export -n $prjname -f $env_file
-
-if [[ $? == 0 ]]; then
-	info "Done. The environment file is $env_file."
-else
-	error "Something went wrong" $?
-fi
diff --git a/bioinfoconda/local/src/X-conda-get-channels.pl b/bioinfoconda/local/src/X-conda-get-channels.pl
deleted file mode 100755
index b843a0e..0000000
--- a/bioinfoconda/local/src/X-conda-get-channels.pl
+++ /dev/null
@@ -1,62 +0,0 @@
-#!/usr/bin/perl
-
-# NOTE: this program is for internal use only.
-# Input: a conda environment file (as recent as possible)
-# Output: the list of channels used in that environment
-
-use strict;
-use warnings;
-use File::Basename;
-use Getopt::Long;
-use YAML::Tiny;
-
-my $NAME = basename($0);
-my $USAGE =<<USAGE;
-Usage: $NAME -f env_file
-
-Options:
-	-f|--file		The yml file containing the environment
-	-h|--help		Print this message.
-
-Notes:
-	Prints the channels of the specified environment, in the priority
-	order. Remember to export the environment to a file before using
-	this script, so that the channel list is updated.
-
-Reporting bugs:
-	federicomarotta AT mail DOT com
-USAGE
-
-# Parse command line options
-my $help = 0;
-my $env_file = '';
-GetOptions(
-        "file|f=s" => \$env_file,
-        "help|h" => \$help
-);
-
-# Print help message
-if ($help)
-{
-        print $USAGE;
-        exit 0;
-}
-
-# Validate arguments
-if ($env_file eq '')
-{
-        die "Error: $USAGE";
-}
-elsif (! -f $env_file)
-{
-        die "Error: $env_file is not a file.\n";
-}
-
-# Open the environment file and parse it
-my $yaml = YAML::Tiny->new;
-$yaml = YAML::Tiny->read($env_file);
-my $channels = $yaml->[0]->{channels};
-
-print "@$channels";
-
-exit 0;
diff --git a/bioinfoconda/local/src/X-conda-get-specs.pl b/bioinfoconda/local/src/X-conda-get-specs.pl
deleted file mode 100755
index 4a3e233..0000000
--- a/bioinfoconda/local/src/X-conda-get-specs.pl
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/usr/bin/perl
-
-# NOTE: this program is for internal use only.
-# Input: a conda history file
-# Output: the list of manually installed packages, excluding manually 
-# removed packages
-
-use strict;
-use warnings;
-use File::Basename;
-use Getopt::Long;
-
-my $NAME = basename($0);
-my $USAGE =<<USAGE;
-Usage: $NAME -f history_file
-
-Options:
-	-f|--file		The history file of the environment
-	-h|--help		Print this message.
-
-Notes:
-	Prints the list of packages to be installed to replicate the
-	environment in its current state.
-
-Reporting bugs:
-	federicomarotta AT mail DOT com
-USAGE
-
-# Parse command line options
-my $help = 0;
-my $history_file = '';
-GetOptions(
-	"file|f=s" => \$history_file,
-	"help|h" => \$help
-);
-
-# Print help message
-if ($help)
-{
-	print $USAGE;
-	exit 0;
-}
-
-# Validate arguments
-if ($history_file eq '')
-{
-	die "Error: $USAGE";
-}
-elsif (! -f $history_file)
-{
-	die "Error: $history_file is not a file.\n";
-}
-
-# Get the specs from history
-open HISTORY, "<", $history_file
-	or die "Error: could not open $history_file: $!";
-my @update_specs;
-while (<HISTORY>)
-{
-        if (m/^# update specs: \[(.*)\]/)
-        {
-                my @specs = split(/, /, $1);
-                foreach my $spec (@specs)
-                {
-                        push(@update_specs, substr($spec, 1, length($spec) - 2));
-                }
-        }
-        elsif (m/^# remove specs: \[(.*)\]/)
-        {
-                my @specs = split(/, /, $1);
-                foreach my $spec (@specs)
-                {
-                        $spec = substr($spec, 1, length($spec) - 2);
-                        for (my $i = 0; $i <= $#update_specs; $i++)
-                        {
-                                if ($update_specs[$i] eq $spec)
-                                {
-                                        splice(@update_specs, $i, 1);
-                                }
-                        }
-                }
-        }
-}
-close(HISTORY);
-@update_specs = uniq(@update_specs);
-
-print "@update_specs";
-
-exit 0;
-
-# https://stackoverflow.com/questions/7651/how-do-i-remove-duplicate-items-from-an-array-in-perl
-sub uniq
-{
-        my %seen;
-        grep !$seen{$_}++, @_;
-}
diff --git a/bioinfoconda/local/src/X-conda-install.sh b/bioinfoconda/local/src/X-conda-install.sh
deleted file mode 100755
index e68a2fb..0000000
--- a/bioinfoconda/local/src/X-conda-install.sh
+++ /dev/null
@@ -1,113 +0,0 @@
-#!/bin/bash
-
-# TODO: we should parse all the options with optparse and validate them.
-
-# validate the environment
-if [[ ! -z "${BIOINFO_ROOT}" ]]; then
-        source $BIOINFO_ROOT/bioinfoconda/local/lib/bash/bash_functions
-else
-	>&2 echo 'ERROR: ${BIOINFO_ROOT} is not defined'
-	exit 3
-fi
-if [[ -z "${CONDA_PREFIX}" ]]; then
-        error 'You must be inside a conda environment' 3
-fi
-
-options=yfmCc:n:p:qkh
-longoptions=help
-
-date=$(date +%Y-%m-%d)
-minicondapath=$(conda info --base)
-prjname=$(basename ${CONDA_PREFIX})
-prjpath=${BIOINFO_ROOT}/prj/$prjname
-env_file=$prjpath/local/condafiles/${prjname}_${date}.yml
-history_file=${CONDA_PREFIX}/conda-meta/history
-argv=$@
-
-# Usage string
-read -r -d '' usage << END
-Usage:
-        X-conda install -c CHANNEL PACKAGE1 PACKAGE2 ...
-
-More in detail:
-    `basename $0` install [-y] [--dry-run] [-f] [--no-deps] [-m]
-            [-C] [--use-local] [--offline] [--no-pin] [-c CHANNEL]
-            [--override-channels] [-n ENVIRONMENT | -p PATH] [-q]
-            [--copy] [-k] [--update-dependencies]
-            [--no-update-dependencies] [--channel-priority]
-            [--no-channel-priority] [--clobber]
-            [--show-channel-urls] [--no-show-channel-urls]
-            [--download-only] [--json] [--debug] [--verbose]
-            [PACKAGE1 [PACKAGE2 [...]]]
-
-Options:
-    For an explanation of the options, see the usage of \`conda
-    create'.
-
-Notes:
-    This program removes and recreate the current conda environment.
-    It is the heavy artillery to be deployed when "conda install"
-    fails. As specified in the documentation of conda, the
-    installation of all the packages at once reduces the chances
-    of conflicts.
- 
-    If you do not provide any option, the environment will be
-    simply regenerated; this might be useful to solve some
-    conda-related problems.
-
-Reporting bugs:
-    federicomarotta AT mail DOT com
-END
-
-PARSER=$(getopt --options=$options --longoptions=$longoptions --name "$0" -- "$@")
-eval set -- "$PARSER"
-
-while true; do
-	case "$1" in
-		-h|--help )
-			echo "$usage"
-			exit 0
-			;;
-                -- )
-			shift
-			break
-			;;
-		* )
-            # For now we do not exclude any argument
-            shift
-			;;
-	esac
-done
-
-# Export the environment as it is now
-X-conda-export
-
-# Get a list of channels and update_specs
-info "Getting the channels and packages of the environment..."
-channels="-c $(X-conda-get-channels -f $env_file | sed 's/ / -c /g')"
-specs=$(X-conda-get-specs -f $history_file)
-
-# Recreate the environment
-info "Deactivating environment..."
-source "$minicondapath/etc/profile.d/conda.sh"
-conda deactivate
-
-info "Running: conda env remove -n $prjname"
-conda env remove -y -q -n $prjname
-
-info "Running: conda create --name $prjname $channels $argv $specs"
-conda create -y --name $prjname $channels $argv $specs
-
-if [[ $? -eq 0 ]]; then
-	# info "Reactivating environment..."
-	info "All done."
-else
-	error "Sorry, that did not work. You can regenerate the environment as it was through $env_file." 9
-fi
-
-# It's not necessary to reactivate the environment, because it was only 
-# deactivated for the shell opened by this script; activating the 
-# environment here would be pointless.
-
-# source activate $prjname
-# info "All done."
diff --git a/bioinfoconda/local/src/X-conda.sh b/bioinfoconda/local/src/X-conda.sh
deleted file mode 100755
index 2a4ec7c..0000000
--- a/bioinfoconda/local/src/X-conda.sh
+++ /dev/null
@@ -1,42 +0,0 @@
-#!/bin/bash
-
-# TODO: allow to run outside of an environment (parse -p and -n options)
-
-# validate the environment
-if [[ ! -z "${BIOINFO_ROOT}" ]]; then
-        source $BIOINFO_ROOT/bioinfoconda/local/lib/bash/bash_functions
-else
-	>&2 echo 'ERROR: ${BIOINFO_ROOT} is not defined'
-	exit 3
-fi
-if [[ -z "${CONDA_PREFIX}" ]]; then
-        error 'You must be inside a conda environment' 3
-fi
-
-# Usage string
-read -r -d '' usage << END
-Usage:
-	`basename $0` [-h] command ...
-
-Commands:
-	The command can be one of the following:
-
-	* install:	brute-force installation of packages
-	* export:	save the environment to a file
-
-Reporting bugs:
-	federicomarotta AT mail DOT com
-END
-
-# Check syntax and acquire options and arguments
-if [[ $# -eq 0 ]]; then
-        error "$usage" 1
-elif [ $1 == "-h" ]; then
-	echo "$usage"
-elif [ $1 == "install" ]; then
-	X-conda-install "${@:2}"
-elif [ $1 == "export" ]; then
-	X-conda-export "${@:2}"
-else
-	error "$usage" 1
-fi
diff --git a/bioinfoconda/local/src/X-getdata.pl b/bioinfoconda/local/src/X-getdata.pl
deleted file mode 100755
index d7f6f2e..0000000
--- a/bioinfoconda/local/src/X-getdata.pl
+++ /dev/null
@@ -1,828 +0,0 @@
-#!/usr/bin/perl
-
-use warnings;
-use strict;
-#use Digest::SHA;
-use Digest::MD5;
-use File::Basename;
-use File::Copy;
-use File::Find;
-use File::Path qw(make_path);
-use Fcntl qw(:flock SEEK_END);
-use Getopt::Long;
-
-# TODO: implement -R option.
-
-# TODO: accept patterns for http too.
-
-# TODO: accept patterns in the middle of the path.
-
-# TODO: check if new dest is overriding something.
-
-# TODO: pass @ARGV as @params for rsync, e.g. to specify port or
-# something else in the command line.
-
-my $NAME = basename($0);
-my $USAGE =<<USAGE;
-Usage: $NAME [options] URL
-   or: $NAME [options] USER\@HOST:PATH
-
-Options:
-	-R|--reject=pattern		Reject files matching pattern. (Not yet implemented)
-	-f|--fix-index			Attempt to interactively fix the data index
-	-h|--help				Print this message.
-
-Notes:
-	URL is the Universal Resource Location of the file to download.
-	$NAME can use either the ftp(s) or the http(s) protocol. In the former
-	case, URLs can contain patterns (such as [], {}, ? and * elements), so
-	that all the files matching the pattern are downloaded; the pattern
-	can be specified only for the filename, not for dirnames.
-
-	If the file is on a remote host (or even in a given location of the local
-	host, use the second syntax, which is similar to the one used by scp
-	and rsync, except that you don't have to provide a destination. Like URL,
-	PATH can contain patterns, but only in the filename, not in the dirname.
-
-	The script automatically suggests a possible location to save the
-	downloads: for instance, if the URL is http://foo.com/boo/bar/baz.vcf.gz,
-	the suggestion will be foo/boo/bar/baz.vcf.gz. You will then be prompted
-	for a new location, where you can provide an alternative path. The
-	suggestions for PATH are somewhat less sophisticated and in 100% of the
-	cases you will want to manually override them.
-
-	If the URL or the remothe PATH end with a trailing /, it is
-	interpreted as /*. The destination path must be relative to the bioinfo
-	data directory, and if it does not exist, then it is created. When the
-	protocol is not specified, it is supposed to be http.
-
-	Each time a file is downloaded, an entry to the index is 
-	appended so that the user who downloaded the file, the time of the 
-	download, the url and the local path are logged. If some files are moved
-	or downloaded manually, the index might become unrepresentative, therefore
-	it has to be fixed manually.
-
-Reporting bugs:
-	federicomarotta AT mail DOT com
-USAGE
-
-# Validate environment
-if (defined $ENV{"BIOINFO_ROOT"} && length($ENV))
-{
-    die("ERROR: \$BIOINFO_ROOT is not defined.\n");
-}
-if (! -d "$ENV{'BIOINFO_ROOT'}/data")
-{
-    die("ERROR: $ENV{'BIOINFO_ROOT'}/data does not exists.\n")
-}
-my $data_root = "$ENV{'BIOINFO_ROOT'}/data/";
-my $index_file = "$ENV{'BIOINFO_ROOT'}/bioinfoconda/local/var/data_index";
-
-# Parse command line options
-my $help = 0;
-my $reject = '';
-my $fix_index = 0;
-GetOptions(
-    "reject|R=s" => \$reject,
-    "fix-index|f" => \$fix_index,
-    "help|h" => \$help
-);
-
-# Print help message
-if ($help)
-{
-    print $USAGE;
-    exit 0;
-}
-
-# Fix index
-if ($fix_index)
-{
-    # Check syntax
-    if (scalar(@ARGV) != 0)
-    {
-        print "You cannot specify an URL when fixing the index.\n";
-        print $USAGE;
-        exit 1;
-    }
-    if ($reject ne '')
-    {
-        print "-f is not compatible with -R.\n";
-        print $USAGE;
-        exit 1;
-    }
-
-    # Try to fix the index
-    fix_index($index_file);
-
-    exit 0;
-}
-
-# By default, download
-# Parse arguments
-if (scalar(@ARGV) != 1)
-{
-	print $USAGE;
-	exit 1;
-}
-my $source = $ARGV[0];
-my @output = ();
-
-# Recognise the protocol
-if ($source =~ m#^https?://# or $source =~ m#^ftps?://#)
-{
-	# Parse the URL
-	my ($protocol, $domain, $port, $path, @params) = parse_url($source);
-	
-	# Validate the URL
-	my $v_source = validate_url($protocol, $domain, $port, $path, \@params);
-
-	# Find an appropriate destination path
-	my $dest = find_dest_url($domain, $path, \@params);
-
-	# Ensure that dest ends with a / for recursive downloads
-	if (is_recursive($v_source) and $dest !~ m/\/$/) {
-		$dest .= "/";
-	}
-	print "\nSaving files to $data_root$dest.\n\n";
-	
-	# Finally download the files
-	if (is_recursive($v_source))
-	{
-	    @output = wget_recursive($v_source, $data_root . $dest);
-	}
-	else
-	{
-	    @output = wget_simple($v_source, $data_root . $dest);
-	}
-}
-elsif ($source =~ m#^rsync://# or $source =~ m/@/)
-{
-	# Parse the hostname
-	my ($protocol, $user, $host, $path) = parse_host($source);
-
-	# Validate the hostname
-	my $v_source = validate_host($protocol, $user, $host, $path);
-
-	# Get an appropriate destination path
-	my $dest = find_dest_host($host, $path);
-
-	# Ensure that dest ends with a / for recursive downloads
-	if (is_recursive($v_source) and $dest !~ m/\/$/) {
-		$dest .= "/";
-	}
-	print "\nSaving files to $data_root$dest.\n\n";
-
-	# Finally download the files
-	if (is_recursive($v_source))
-	{
-		@output = rsync_recursive($v_source, $data_root . $dest);
-	}
-	else
-	{
-		@output = rsync_simple($v_source, $data_root . $dest);
-	}
-}
-else
-{
-	die("ERROR: unrecognised source. Please specify the protocol or the username\@host.\n");
-}
-
-if (@output)
-{
-	# Add an entry to the index file
-	print "Updating index...\n";
-	update_index(\@output);
-
-	# Remove write permissions to everybody
-	for (my $i = 0; $i < scalar(@output); $i += 4)
-	{
-	    chmod(0444, $output[$i+3]);
-	}
-}
-
-print "Done.";
-exit 0;
-
-# Subroutines
-
-sub parse_url
-{
-	my $url = $_[0];
-
-	my @parsed_url = ($url =~ m#^((.*)://)?(.*?)(:(\d+))?(/.*?)(\?(.+))?$#);
-	my @path = split(//, $parsed_url[5]);
-
-	for (my $i = 0; $i < scalar(@parsed_url); $i++)
-	{
-		if (! $parsed_url[$i])
-		{
-			$parsed_url[$i] = '';
-		}
-	}
-	if (! $parsed_url[1])
-	{
-		$parsed_url[1] = "http";
-	}
-
-	# If url has a trailing slash, download recursively
-	if ($path[-1] eq '/')
-	{
-		$parsed_url[5] .= '*';
-	}
-	my @params = split(/&/, $parsed_url[6]);
-
-	# The fields are as follows: protocol, domain name, port, path, query parameters
-	return ($parsed_url[1], $parsed_url[2], $parsed_url[4], $parsed_url[5], @params);
-}
-
-sub parse_host
-{
-	my $host = $_[0];
-
-	my @parsed_host = ($host =~ m#^((.*)://)?((.*)@)?(.*?)(:(.*))$#);
-	my @path = split(//, $parsed_host[6]);
-
-	for (my $i = 0; $i < scalar(@parsed_host); $i++)
-	{
-		if (! $parsed_host[$i])
-		{
-			$parsed_host[$i] = '';
-		}
-	}
-
-	# If the path has a trailing slash, download recursively
-	if ($path[-1] eq '/')
-	{
-		$parsed_host[6] .= '*';
-	}
-
-	# The fields are as follows: username, hostname, path
-	return ($parsed_host[1], $parsed_host[3], $parsed_host[4], $parsed_host[6]);
-}
-
-sub validate_url
-{
-	my $protocol = $_[0];
-	my $domain = $_[1];
-	my $port = $_[2];
-	my $path = $_[3];
-	my @params = @{$_[4]};
-	my $v_url = '';
-	
-	# TODO: other validations
-	
-	if ($protocol =~ m/^http/)
-	{
-		# Path cannot contain patterns
-		if ($path =~ m/[\*\?\[\]\{\}]/)
-		{
-			die("ERROR: path cannot contain patterns if the protocol is http.\n");
-		}
-	}
-	elsif ($protocol =~ m/^ftp/)
-	{
-		# Only the last item can contain patterns
-		my @path = split(/\//, $path);
-		for (my $i = 0; $i < scalar(@path); $i++)
-		{
-			if ($path[$i] =~ m/[\*\?\[\]\{\}]/ and $i != $#path)
-			{
-				die("ERROR: metacharacters are allowed only for file names, not for directories.\n");
-			}
-		}
-	}
-	else
-	{
-		die("ERROR: protocol $protocol is not supported.\n");
-	}
-	
-	# Recompose the URL
-	$v_url = $protocol . "://" . $domain;
-	if ($port)
-	{
-		$v_url .= ":" . $port;
-	}
-	$v_url .= $path;
-	if (@params)
-	{
-		$v_url .= "?" . join('&', @params);
-	}
-	
-	return $v_url;
-}
-
-sub validate_host
-{
-	my $protocol = $_[0];
-	my $username = $_[1];
-	my $hostname = $_[2];
-	my $path = $_[3];
-	my $v_host = '';
-
-	if ($username eq '')
-	{
-		$username = $ENV{USERNAME};
-	}
-	if ($path eq '')
-	{
-		die("ERROR: please provide the path of the file.\n");
-	}
-
-	# Only the last item can contain patterns
-	my @path = split(/\//, $path);
-	for (my $i = 0; $i < scalar(@path); $i++)
-	{
-		if ($path[$i] =~ m/[\*\?\[\]\{\}]/ and $i != $#path)
-		{
-			die("ERROR: metacharacters are allowed only for file names, not for directories.\n");
-		}
-	}
-
-	if ($protocol)
-	{
-		$v_host .= $protocol . "://";
-	}
-
-	$v_host .=  $username . "@" . $hostname . ":" . $path;
-	return $v_host;
-}
-
-sub find_dest_url
-{
-	my $domain = $_[0];
-	my $path = $_[1];
-	my @params = @{$_[2]};
-
-	# Extract the first meaningful level domain
-	my @levels = split(/\./, $domain);
-	my $fld = '';
-	for (my $i = 0; $i < scalar(@levels); $i++)
-	{
-		if (is_prefix($levels[$i]) || is_pseudo($levels[$i]))
-		{
-			next;
-		}
-		else
-		{
-			$fld = $levels[$i];
-			last;
-		}
-	}
-
-	# Extract a path
-	my @dirs = split(/\//, $path);
-	my $localdirs = '';
-	for (my $i = 1; $i < scalar(@dirs); $i++)
-	{
-		if (is_pseudo($dirs[$i]))
-		{
-			next;
-		}
-		elsif ($dirs[$i] =~ m/[\*\?\[\]\{\}]/)
-		{
-			$localdirs .= '/';
-			last;
-		}
-		else
-		{
-			$localdirs .= '/' . $dirs[$i];
-		}
-	}
-
-	# Add params
-	if (@params)
-	{
-		for (my $i = 0; $i < scalar(@params); $i++)
-		{
-			my @value = split(/=/, $params[$i]);
-			$localdirs .= '/' . $value[1];
-		}
-	}
-
-	# Recompose the destination path
-	my $tmp_dest = $fld . $localdirs;
-	$tmp_dest =~ s#^/##;
-
-	# Manually override the proposed destination
-	my $dest = edit_dest($tmp_dest);
-
-	return $dest;
-}
-
-sub find_dest_host
-{
-	my $host = $_[0];
-	my $path = $_[1];
-
-	# Extract a path
-	my @dirs = split(/\//, $path);
-	my $localdirs = '/';
-	for (my $i = 1; $i < scalar(@dirs); $i++)
-	{
-		if ($dirs[$i] =~ m/[\*\?\[\]\{\}]/)
-		{
-			$localdirs .= '/';
-			last;
-		}
-		else
-		{
-			$localdirs .= '/' . $dirs[$i];
-		}
-	}
-
-	my $tmp_dest = $host . $localdirs;
-	my $dest = edit_dest($tmp_dest);
-
-	return $dest;
-}
-
-sub edit_dest
-{
-        my $dest = $_[0];
-        my $tmp_dest = '';
-
-        print "\nThe suggested path for the files is $dest\n";
-
-        print "\nIn order to maintain a systematic ordering of the directories, the \
-destination path should be a subpath of the url (for instance, if the url is \
-https://www.foo.com/bar/baz/bin/a.txt, a suitable destination could be \
-foo/bin/a.txt, if bar/baz is not relevant.\n";
-
-        print "\nEnter an empty line if the suggested path is good, otherwise type a path \
-(relative to $data_root):\n";
-
-        while (my $tmp_dest = <STDIN>)
-        {
-                chomp $tmp_dest;
-
-                if ($tmp_dest ne '')
-                {
-                        if (is_valid_dest($tmp_dest))
-                        {
-                                system("echo \"$ENV{USER}: Overridding suggested path $dest with new path $tmp_dest.\" | systemd-cat -t $NAME -p notice");
-                                $dest = $tmp_dest;
-                                last;
-                        }
-                        else
-                        {
-                                print "The path must be relative to $data_root, and cannot contain '..'.\nTry again:\n";
-                                next;
-                        }
-                }
-                else
-                {
-                        last;
-                }
-        }
-
-        return $dest;
-}
-
-sub wget_simple
-{
-    my $url = $_[0];
-    my $dest = $_[1];
-    my $dirname = dirname($dest);
-    my @output = (0);
- 
-    unless(-d $dirname or make_path($dirname))
-    {
-        die("ERROR: cannot make path $dirname.\n");
-    }
- 
-    open(WGETOUTPUT, "wget -O $dest $url 2>&1 |");
-    while (my $line = <WGETOUTPUT>)
-    {
-        # update the progress line...
-        if ($line =~ m/^\s*\d+[KMGT]\s+/)
-        {
-            chomp $line;
-            print "\r$line";
-            # put back the "\n" to the last line
-            if ($line =~ m/100%/)
-            {
-                print "\n";
-            }
-        }
-        # ...and append the other lines
-        else
-        {
-            print $line;
-            # extract the information to be logged
-            if ($line =~ m/ saved \[.*\]/)
-            {
-                # We want @output to contain: date, 
-                # hour, url, path. But wget simple 
-                # returns only date, hour, path, so we 
-                # add the url.
-                @output = ($line =~ m/(.*) (.*) \(.*\) - '(.*)' saved \[.*\]/);
-                splice(@output, 2, 0, $url);
-            }
-        }
-    }
- 
-    return @output;
-}
-
-sub wget_recursive
-{
-        my $url = $_[0];
-        my $dest = $_[1];
-		# my $dirname = dirname($dest);
-		my $dirname = $dest;
-        my @output = ();
-        my @urldirs = split("/", $url);
-        my $cutdirs;
-
-        unless(-d $dirname or make_path($dirname))
-        {
-                die("ERROR: cannot make path $dirname.\n");
-        }
-
-		$cutdirs = $#urldirs-2;
-        # we subtract the false dirs generated by ://
-        open(WGETOUTPUT, "wget -P $dirname \\
-                -N --no-verbose --show-progress \\
-                -r -l inf --no-parent \\
-                -nH --cut-dirs=$cutdirs \\
-                $url 2>&1 |");
-        while (my $line = <WGETOUTPUT>)
-        {
-                # update the progress line...
-                if ($line =~ m/^\s*\d+[KMGT]\s+/ and $line =~ m/%/)
-                {
-                        chomp $line;
-                        print "\r$line";
-                        # put back the "\n" to the last line
-                        if ($line =~ m/100%/)
-                        {
-                                print "\n";
-                                # extract the information to be logged
-                                if ($line !~ m/.listing/)
-                                {
-                                        push @output, ($line =~ m/100% .*(....-..-..) (.*) URL: (.*) \[\d+\] -> "(.*)" \[\d+\]$/);
-                                }
-                        }
-                }
-                # ...and append the other lines
-                else
-                {
-                        print $line;
-                }
-        }
-
-        return @output;
-}
-
-sub rsync_simple
-{
-	my $source = $_[0];
-	my $dest = $_[1];
-	my $dirname = dirname($dest);
-	my @output = ();
-
-	unless(-d $dirname or make_path($dirname))
-	{
-		die("ERROR: cannot make path $dirname.\n");
-	}
-
-	open(RSYNCOUTPUT, "rsync -rtvz --out-format=\"%t %f\" $source $dest 2>&1 |");
-	while (my $line = <RSYNCOUTPUT>)
-	{
-		if ($line =~ m/^\d{4}\/\d{2}\/\d{2}/)
-		{
-			chomp($line);
-			$line .= " " . $dest . "\n";
-			my @line = split(" ", $line);
-			$line[2] = $source;
-			push @output, @line;
-		}
-		print $line;
-	}
-
-	return @output;
-}
-
-sub rsync_recursive
-{
-	my $source = $_[0];
-	my $dest = $_[1];
-	my $dirname = dirname($dest);
-	my @output = ();
-
-	unless(-d $dirname or make_path($dirname))
-	{
-		die("ERROR: cannot make path $dirname.\n");
-	}
-
-	open(RSYNCOUTPUT, "rsync -rtvz --out-format=\"%t %f\" $source $dest 2>&1 |");
-	while (my $line = <RSYNCOUTPUT>)
-	{
-		if ($line =~ m/^\d{4}\/\d{2}\/\d{2}/)
-		{
-			chomp($line);
-			$line .= " " . $dest . "\n";
-			my @line = split(" ", $line);
-			$line[3] = $line[3] . $line[2];
-			$line[2] = dirname($source) . "/" . $line[2];
-			push @output, @line;
-		}
-		print $line;
-	}
-
-	return @output;
-}
-
-sub update_index
-{
-    my @log = @{$_[0]};
-    #my $ctx = Digest::SHA->new(1);
-    my $ctx = Digest::MD5->new;
-
-    open(INDEXFILE, ">>", $index_file)
-	    or die "ERROR: cannot open $index_file.";
-
-    for (my $i = 0; $i < scalar(@log); $i += 4)
-    {
-        # @log contains, for each file, date, hour, url, path. 
-		# Logs for different files are stored sequentially, in a 
-		# flat fashion.
-
-        # Compute checksum for each downloaded file
-        my $digest = checksum($ctx, $log[$i+3]);
-
-        # Append line to the index
-        print INDEXFILE "$log[$i] $log[$i+1]\t$ENV{USER}\t$log[$i+2]\t$log[$i+3]\t$digest\n";
-    }
-
-    close(INDEXFILE);
-}
-
-sub fix_index
-{
-        my $index_file = $_[0];
-        #my $ctx = Digest::SHA->new(1);
-        my $ctx = Digest::MD5->new;
-
-        # Backup the previous index
-        copy($index_file, $index_file.".old") or die "Failed to backup index file: $!";
-
-	# Actual files under $data_root
-        my %tree;
-        my %tree_bypath;
-	find(sub {
-                return unless -f;       # Must be a file
-                return if /^\./;	# Must not be hidden
-
-                my $date = substr(`stat -c '%y' $File::Find::name`, 0, 19);
-                my $user = (getpwuid((stat $File::Find::name)[4]))[0];
-                my $digest = checksum($ctx, $File::Find::name);
-
-                $tree{$digest} = [$date, $user, $File::Find::name, $File::Find::name];
-                $tree_bypath{$File::Find::name} = [$date, $user, $File::Find::name, $digest];
-
-	}, $data_root);
-
-        # Files in the index
-        my %index;
-        my %index_bypath;
-        open(INDEXFILE, "+<", $index_file) or die "ERROR: cannot open $index_file: $!";
-        flock(INDEXFILE, LOCK_EX) or die "Cannot lock $index_file: $!";
-	while (<INDEXFILE>)
-        {
-                chomp;
-                @_ = split /\t/;
-                $index{$_[4]} = [$_[0], $_[1], $_[2], $_[3]];
-                $index_bypath{$_[3]} = [$_[0], $_[1], $_[2], $_[4]];
-        }
-
-        # Find checksums in common and check if they have the same path
-        foreach my $checksum (keys(%tree))
-        {
-                if (! exists $index{$checksum})
-                {
-                        # We have to add this file to the index
-                        $index{$checksum} = $tree{$checksum};
-                }
-                elsif ($tree{$checksum}[3] ne $index{$checksum}[3])
-                {
-                        # We have to rename this file in the index
-                        $index{$checksum}[3] = $tree{$checksum}[3];
-                        $index{$checksum}[0] = $tree{$checksum}[0];
-                }
-        }
-
-        # Find checksums only in the index
-        foreach my $checksum (keys(%index))
-        {
-                if (! exists($tree{$checksum}))
-                {
-                        # We have to delete the files from the index
-                        delete($index{$checksum});
-                }
-        }
-
-        # Now check if the files with the same path have actually the 
-        # same checksum
-        foreach my $path (keys(%tree_bypath))
-        {
-                if (exists($index_bypath{$path}) and $tree_bypath{$path}[3] ne $index_bypath{$path}[3])
-                {
-                        # We have a problem
-                        print "Attention! The file $path may be corrupted.\n";
-                }
-        }
-
-        # Print the new healthy index
-        seek(INDEXFILE, 0, 0);
-        truncate(INDEXFILE, 0);
-        foreach my $checksum (keys(%index))
-        {
-                print INDEXFILE "$index{$checksum}[0]\t$index{$checksum}[1]\t$index{$checksum}[2]\t$index{$checksum}[3]\t$checksum\n";
-        }
-        close(INDEXFILE);
-
-        return 0;
-}
-
-sub checksum
-{
-    my $ctx = $_[0];
-    my $path = $_[1];
-
-    # MD5 algorithm
-    open(my $fh, "<", $path)
-            or die "Could not open $path.";
-    $ctx->addfile($fh);
-    my $digest = $ctx->hexdigest;
-
-    close($fh);
-    return $digest;
-
-    # SHA algorithm
-    #$ctx->addfile($path);
-    #my $digest = $ctx->hexdigest;
-
-    #return $digest;
-}
-
-sub is_valid_dest
-{
-        my $dest = $_[0];
-
-        if ($dest =~ m#^/#)
-        {
-                return 0;
-        }
-        if ($dest =~ m#\.\./#)
-        {
-                return 0;
-        }
-
-        return 1;
-}
-
-sub is_prefix
-{
-        my $level = $_[0];
-
-        # list of prefixes
-        # soe: ucsc
-        # cse: ucsc
-        my @prefixes = ("www", "ftp", "soe", "cse", "com");
-
-        for (my $i = 0; $i < scalar(@prefixes); $i++)
-        {
-                if ($level eq $prefixes[$i])
-                {
-                        return 1;
-                }
-        }
-
-        return 0;
-}
-
-sub is_pseudo
-{
-        my $dir = $_[0];
-        my @pseudodirs = ("pub", ".*?download.*?", "tmp", "files", 
-                "goldenPath", "ftp", "databases", "storage", "googleapis");
-
-        for (my $i = 0; $i < scalar(@pseudodirs); $i++)
-        {
-                if ($dir =~ m/$pseudodirs[$i]/i)
-                {
-                        return 1;
-                }
-        }
-
-        return 0;
-}
-
-sub is_recursive
-{
-	my $path = $_[0];
-
-	return ($path =~ m/[\*\?\[\]\{\}]/);
-}
diff --git a/bioinfoconda/local/src/X-mkprj.sh b/bioinfoconda/local/src/X-mkprj.sh
deleted file mode 100755
index 5b1b081..0000000
--- a/bioinfoconda/local/src/X-mkprj.sh
+++ /dev/null
@@ -1,545 +0,0 @@
-#!/bin/bash
-
-# TODO: save templates as files and default environment as yml.
-
-# TODO: improve documentation of -l.
-
-# TODO: use relative paths inside a project.
-
-# validate the environment
-if [[ -z "${BIOINFO_ROOT}" ]]; then
-    error '${BIOINFO_ROOT} is not defined' 3
-fi
-
-source $BIOINFO_ROOT/bioinfoconda/local/lib/bash/bash_functions
-
-if which conda > /dev/null; then
-    minicondapath=$(conda info --base)
-fi
-bioinfotreepath="$BIOINFO_ROOT/bioinfotree"
-gitlab_config_file="$BIOINFO_ROOT/bioinfoconda/local/etc/gitlab"
-
-options=hTGlCir
-longoptions=help,no-templates,no-git,gitlab,no-conda,interactive-conda,remove
-
-# Usage string
-read -r -d '' usage << END
-Usage: `basename $0` [options] prjname
-
-Options:
-    -T|--no-templates       do not create template Snakefile and
-                            Dockerfile.
-    -G|--no-git             do not initialise local git repository.
-    -l|--gitlab             create remote gitlab repository.
-    -C|--no-conda           do not create the conda environment.
-    -i|--interactive-conda  enable the creation of a customised conda
-                            environment.
-    -r|--remove             remove project directory and conda
-                            environment.
-    -h|--help               print this message.
-
-Notes:
-    This program does the following things:
-    1) Creating a directory structure for the project.
-    2) Adding default Dockerfile and Snakefile.
-    3) Initialising a git repository.
-    4) Creating a conda environment.
-    5) Setting up direnv for project environment and libraries.
-
-    With the \`-i' option, you will be prompted to choose the channels
-    and packages that will be added initially to the conda environment;
-    otherwise the environment will contain R, perl, cpanm and snakemake.
-    Use this option only if you know what you are doing.
-
-    The \`-l' option is used to create a remote repository on gitlab
-    and associate it to the local repository. (If you pass this
-    option together with -r, the gitlab repository is deleted; see
-    below.)
-
-    To remove a project, use the \`-r' option and provide the
-    project name. The entire directory of the project, as well as
-    the related conda environment, if it exists, are eliminated. If
-    you also pass the -l option, the remote gitlab repository is
-    deleted too, if it exists.
-
-Reporting bugs:
-    federicomarotta AT mail DOT com
-END
-
-# Functions definition
-function clean_prj()
-{
-    prjpath=$1
-    prjname=$(basename $prjpath)
-    gitlab_username=$( awk '(NR == 2) {print $1}' $gitlab_config_file )
-    gitlab_group_id=$( awk '(NR == 2) {print $2}' $gitlab_config_file )
-    gitlab_token=$( awk '(NR == 2) {print $3}' $gitlab_config_file )
-
-    # Remove local directory
-    if [ -d $prjpath ]; then
-        rm -rf $prjpath
-    fi
-
-    # Remove conda environment
-    if conda info --envs | grep "^$prjname[[:space:]]" > /dev/null; then
-        conda env remove -y -n $prjname
-    fi
-
-    # Remove remote gitlab repository
-    if ((gitlab)); then
-        # Check for invalid gitlab configuration
-        if [ -z "$gitlab_username" ] || [ -z "$gitlab_group_id" ] || [ -z "$gitlab_token" ]; then
-            echo "Invalid gitlab configuration. This feature requires 
-            you to provide some configuration parameters; check the 
-            documentation for help."
-            return 4
-        fi
-        curl -s --header "Private-Token: $gitlab_token" \
-            -X DELETE "https://gitlab.com/api/v4/projects/$gitlab_username%2F$prjname"
-    fi
-
-    #response=$( curl -s --header "Private-Token: $gitlab_token" \
-            #-X DELETE "https://gitlab.com/api/v4/projects/" \
-            #-d "name=$prjname" | jq -r ".message" )
-
-    #if [ "$?" != "0" ]; then
-            #echo "curl had some problems to send your request."
-            #return $?
-    #fi
-    #if [ "$response" != "null" ]; then
-            #echo "The GitLab API complained about your request:"
-            #echo $response
-            #return 8
-    #fi
-
-    return 0
-}
-function is_valid_name()
-{
-    re='^[0-9a-z_-]+$'
-    if [[ $1 =~ $re ]] ; then
-        return 0
-    else
-        return 1
-    fi
-}
-function make_dirs()
-{
-    prjpath=$1
-
-    mkdir -p $prjpath/dataset \
-        && mkdir -p $prjpath/local/{R,benchmark,bin,builds,config,data,doc,dockerfiles,lib,log,python,snakefiles,src,tmp,condafiles} \
-        && mkdir -p $prjpath/local/lib/{perl5,python,R} \
-    || return $?
-
-    configure_direnv_local $prjpath
-
-    return 0
-}
-function create_templates()
-{
-    prjpath=$1
-    prjname=$(basename $prjpath)
-
-    cat <<- END > $prjpath/local/dockerfiles/Dockerfile
-	# Use the bioinfoconda parent image
-	# NOTE: you should set a version tag!
-	FROM cbuatmbc/bioinfoconda
-	
-	# Copy the project directory into the container
-	# NOTE: remember to add the Snakefiles to the .dockerignore
-	COPY . $prjpath
-	
-	# Create the conda environment from the yml file
-	# NOTE: remember to export the environment before building the 
-	# image, and to edit the following path with the new file.
-	RUN conda env create -f $prjpath/local/condafiles/$prjname.yml
-	
-	RUN chown -R root:bioinfo /bioinfo \
-	    && chmod -R 2777 /bioinfo
-	
-	# Set up the environment
-	ENV PATH="$minicondapath/envs/$prjname/bin:$prjpath/local/bin:\$PATH" \\
-	    PERL5LIB="$prjpath/local/lib/perl:$bioinfotreepath/local/lib/perl" \\
-	    PERL_CPANM_HOME="$prjpath/local/builds/perl5" \\
-	    PERL_CPANM_OPT="-l $prjpath/local --no-man-pages --save-dists=$prjpath/local/src/perl5" \\
-	    PYTHONPATH="$prjpath/local/lib/python:$bioinfotreepath/local/lib/python" \\
-	    R_PROFILE_USER="$prjpath/.Rprofile" \\
-	    CONDA_DEFAULT_ENV="$prjname" \\
-	    CONDA_PREFIX="$minicondapath/envs/$prjname"
-	
-	# Establish the entry point
-	ENTRYPOINT ["$prjpath/local/dockerfiles/docker-entrypoint.sh"]
-	CMD ["snakemake --dag -Tsvg > dag.svg"]
-	END
-
-    cat <<- END > $prjpath/local/dockerfiles/docker-entrypoint.sh
-	#!/usr/bin/env bash
-	cd $prjpath/dataset
-	eval "\$@"
-	END
-
-    cat <<- END > $prjpath/local/dockerfiles/dockerignore
-	# Exclude some hidden files
-	.gitignore
-	.Rproj.user
-	.Rhistory
-	.envrc
-	# Exclude dataset and local/data (this speeds up the build time)
-	dataset/*
-	local/data/*
-	END
-
-    cat <<- END > $prjpath/local/snakefiles/Snakefile
-	# This is a template Snakefile, change it at will
-
-	# Set the config file
-	configfile: "../local/config/snakemake_config.yml"
-
-	# Define the final targets: all the others depend on them
-	ALL = ["foo.bed", "bar.png"]
-
-	# Run the entire pipeline
-	rule all:
-		input: ALL
-	END
-
-    cat <<- END > $prjpath/local/config/snakemake_config.yml
-	BIOINFOCONDA:
-	    ROOT:
-	        "$BIOINFO_ROOT/"
-	    DATA:
-	        "$BIOINFO_ROOT/data/"
-
-	PRJ:
-	    ROOT:
-	        "$prjpath/"
-	    DATA:
-	        "$prjpath/local/data/"
-	END
-
-    ln -s ../local/snakefiles/Snakefile $prjpath/dataset/Snakefile
-    #ln -s local/dockerfiles/Dockerfile $prjpath/Dockerfile
-    ln -s local/dockerfiles/dockerignore $prjpath/.dockerignore
-
-    return 0
-}
-function initialise_repo()
-{
-    prjpath=$1
-
-    git init --shared=group $prjpath > /dev/null || return $?
-	echo .RData > $prjpath/.gitignore
-	echo .Rhistory >> $prjpath/.gitignore
-	echo .Rproj.user >> $prjpath/.gitignore
-	echo dataset/* >> $prjpath/.gitignore
-	echo !dataset/Snakefile >> $prjpath/.gitignore
-	echo local/benchmark/* >> $prjpath/.gitignore
-	echo local/data/* >> $prjpath/.gitignore
-	echo local/log/* >> $prjpath/.gitignore
-	echo local/tmp/* >> $prjpath/.gitignore
-
-    return 0
-}
-function initialise_gitlab_repo()
-{
-    prjpath=$1
-    prjname=$(basename $prjpath)
-    gitlab_username=$( awk '(NR == 2) {print $1}' $gitlab_config_file )
-    gitlab_group_id=$( awk '(NR == 2) {print $2}' $gitlab_config_file )
-    gitlab_token=$( awk '(NR == 2) {print $3}' $gitlab_config_file )
-
-    # Check for invalid configuration
-    if [ -z "$gitlab_username" ] || [ -z "$gitlab_group_id" ] || [ -z "$gitlab_token" ]; then
-        echo "Invalid gitlab configuration. This feature requires you to 
-        provide some configuration parameters; check the documentation 
-        for help."
-        return 4
-    fi
-
-    # Create repository
-    response=$( curl -s --header "Private-Token: $gitlab_token" \
-        -X POST "https://gitlab.com/api/v4/projects" \
-        -d "name=$prjname" | jq -r ".message" )
-
-    if [ "$?" != "0" ]; then
-        echo "curl had some problems to send your request."
-        return $?
-    fi
-    if [ "$response" != "null" ]; then
-        echo "The GitLab API complained about your request:"
-        echo $response
-        return 8
-    fi
-
-    # Share the project with the group
-    response=$( curl -s --header "Private-Token: $gitlab_token" \
-        -X POST "https://gitlab.com/api/v4/projects/$gitlab_username%2F$prjname/share" \
-        -d "group_id=$gitlab_group_id" \
-        -d "group_access=40" | jq -r ".message" )
-
-    if [ "$?" != "0" ]; then
-        echo "curl had some problems to send your request."
-        return $?
-    fi
-    if [ "$response" != "null" ]; then
-        echo "The GitLab API complained about your request:"
-        echo $response
-        return 8
-    fi
-
-    # Add the remote origins
-    cd $prjpath
-    git remote add origin "https://gitlab.com/$gitlab_username/$prjname.git"
-    git remote add ssh-origin "git@gitlab.com:$gitlab_username/$prjname.git"
-    cd $OLDPWD
-
-    return 0
-}
-function create_default_conda()
-{
-    prjpath=$1
-    prjname=$(basename $prjpath)
-    date=$(date +%Y-%m-%d)
-
-    conda create -y --name $prjname -c r -c conda-forge -c bioconda r-base r-essentials perl perl-app-cpanminus snakemake \
-        && conda config --file $minicondapath/envs/$prjname/.condarc --add channels r --add channels conda-forge --add channels bioconda \
-		&& conda env export -n $prjname -f $prjpath/local/condafiles/${prjname}_${date}.yml \
-	|| return $?
-
-    configure_direnv_conda $prjpath
-
-    return 0
-}
-function create_custom_conda()
-{
-    prjpath=$1
-    prjname=$(basename $prjpath)
-    date=$(date +%Y-%m-%d)
-
-    echo "Complete the command, then press enter to run it:"
-    while read -p "conda create -y --name $prjname " args; do
-        if ! conda create -y --name $prjname $args; then
-            echo "That did not work. Please try again:"
-        else
-			conda env export -n $prjname -f $prjpath/local/condafiles/${prjname}_${date}.yml
-            echo "Success!"
-            break
-        fi
-    done
-
-    configure_direnv_conda $prjpath
-
-    return 0
-}
-function configure_direnv_conda()
-{
-    prjpath=$1
-    prjname=$(basename $prjpath)
-
-    echo "source activate $prjname" >> "$prjpath/.envrc"
-    # It is important that the miniconda libraries come last.
-    echo ".libPaths( c(.libPaths(), \"$minicondapath/envs/$prjname/lib/R/library\") )" >> $prjpath/.Rprofile
-}
-function configure_direnv_local()
-{
-    prjpath=$1
-
-    echo "export PATH=$prjpath/local/bin:\$PATH" > "$prjpath/.envrc"
-    echo "export PERL5LIB=$prjpath/local/lib/perl5" >> "$prjpath/.envrc"
-    echo "export PERL_CPANM_HOME=$prjpath/local/builds/perl5" >> "$prjpath/.envrc"
-    echo "export PERL_CPANM_OPT=\"-l $prjpath/local --no-man-pages --save-dists=$prjpath/local/src/perl5\"" >> "$prjpath/.envrc"
-    echo "export PYTHONPATH=$prjpath/local/lib/python" >> "$prjpath/.envrc"
-    echo "export R_PROFILE_USER=$prjpath/.Rprofile" >> "$prjpath/.envrc"
-    echo ".libPaths( c(\"$prjpath/local/lib/R\", .libPaths()) )" > $prjpath/.Rprofile
-}
-
-# check syntax and acquire options and arguments
-PARSER=$(getopt --options=$options --longoptions=$longoptions --name "$0" -- "$@")
-eval set -- "$PARSER"
-
-templates=1
-git=1
-gitlab=0
-conda=1
-interactive=0
-remove=0
-while true; do
-    case "$1" in
-        -h|--help )
-            echo "$usage"
-            exit 0
-            ;;
-        -T|--no-templates )
-            templates=0
-            shift
-            ;;
-        -G|--no-git )
-            git=0
-            shift
-            ;;
-        -l|--gitlab )
-            gitlab=1
-            shift
-            ;;
-        -C|--no-conda )
-            conda=0
-            shift
-            ;;
-        -i|--interactive-conda )
-            interactive=1
-            shift
-            ;;
-        -r|--remove )
-            remove=1
-            shift
-                        ;;
-        -- )
-            shift
-            break
-            ;;
-        * )
-            bug "Unexpected arguments problem."
-            ;;
-    esac
-done
-
-# validate the options
-if ((remove)); then
-    if [[ $templates == 0 || $conda == 0 || $git == 0 || $interactive == 1 ]]; then
-        error "-r is not compatible with any other option (except -l)." 5
-    fi
-fi
-if ! ((git)) && (($gitlab)); then
-    error "-G is not compatible with -l." 5
-fi
-
-# parse and validate the arguments
-if [[ $# -eq 1 ]]; then
-    if ! is_valid_name $1; then
-        error "Project name is not valid. Only lowercase letters, numbers, dashes and underscores are allowed." 5
-    fi
-        if ((remove)); then
-            if ! [ -e ${BIOINFO_ROOT}/prj/$1 ]; then
-                error "This project does not exist." 7
-            fi
-        else
-            if [ -e ${BIOINFO_ROOT}/prj/$1 ]; then
-                error "A project with this name already exists." 7
-            fi
-    fi
-    prjpath=${BIOINFO_ROOT}/prj/$1
-else
-    error "$usage" 1
-fi
-
-# start the script
-
-# Remove a project
-if ((remove)); then
-    prjname=$(basename $prjpath)
-
-    echo "Are you sure you want to remove project \"$prjname\"? Choose y/n."
-    echo "y) Yes, get rid of it!    n) No, wait! Let me reconsider..."
-
-    while read answer; do
-        case ${answer:0:1} in
-            'y'|'Y' )
-                echo
-                info "Removing project $prjpath..."
-                echo
-                clean_prj $prjpath
-                info "All done. The project no longer exists."
-                break
-                ;;
-            'n'|'N'|'' )
-                echo
-                info "OK, the project is safe. Bye"
-                break
-                ;;
-            * )
-                echo -n "Please answer yes or no. Try again: [yes/no] "
-                ;;
-        esac
-    done
-
-    exit
-fi
-
-# Otherwise create a project
-info "Creating project at $prjpath..."
-
-# make directories
-if ! make_dirs $prjpath; then
-    clean_prj $prjpath
-    error "Could not create directories." 9
-fi
-
-# add links to dockerfiles and snakefiles
-if ((templates)); then
-    info "Adding templates for Dockerfile and Snakefile..."
-    if ! create_templates $prjpath; then
-        clean_prj $prjpath
-        error "Could not create links to templates." 9
-    fi
-fi
-
-# initialise a git repository
-if ((git)); then
-        info "Initialising local git repository..."
-    if ! initialise_repo $prjpath; then
-        clean_prj $prjpath
-        error "Could not initialise git repository." 9
-    fi
-fi
-
-# create remote gitlab repository
-if ((gitlab)); then
-    info "Creating remote repository on GitLab..."
-    if ! initialise_gitlab_repo $prjpath; then
-        warn "Could not create remote repository."
-    fi
-fi
-
-# create a conda environment
-if ((conda)); then
-    info "Starting the creation of a conda environment..."
-
-    if ! ((interactive)); then
-        if ! create_default_conda $prjpath; then
-            clean_prj $prjpath
-            error "Could not create conda environment." 9
-        fi
-    else
-        echo "Do you want to create a custom conda environment? Choose y/n."
-        echo "y) create custom environment           n) accept default"
-
-        while read answer; do
-            case ${answer:0:1} in
-                'y'|'Y' )
-                    if ! create_custom_conda $prjpath; then
-                        clean_prj $prjpath
-                        error "Could not create conda environment." 9
-                    fi
-                    break
-                    ;;
-                'n'|'N'|'' )
-                    if ! create_default_conda $prjpath; then
-                        clean_prj $prjpath
-                        error "Could not create conda environment." 9
-                    fi
-                    break
-                    ;;
-                * )
-                    echo -n "Please answer yes or no. Try again: [yes/no] "
-                    ;;
-            esac
-        done
-    fi
-fi
-
-# whitelist directory for direnv
-direnv allow "$prjpath"
-
-info "All done. New project is at $prjpath"
-exit