Merge branch 'develop' into 'master'

Release v0.3.0

See merge request tron/addannot!61

.gitignore

@@ -5,4 +5,5 @@ venv
 .env
 build
 dist
-input.egg-info/
+neofox.egg-info/
+neofox/tests/resources/output*

.gitlab-ci.yml

@@ -0,0 +1,54 @@
+##
+## Copyright (c) 2020-2030 Translational Oncology at the Medical Center of the Johannes Gutenberg-University Mainz gGmbH.
+##
+## This file is part of Neofox
+## (see https://github.com/tron-bioinformatics/neofox).
+##
+## This program is free software: you can redistribute it and/or modify
+## it under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 3 of the License, or
+## (at your option) any later version.
+##
+## This program is distributed in the hope that it will be useful,
+## but WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with this program. If not, see <http://www.gnu.org/licenses/>.##
+image: python:3.7-buster
+
+# Change pip's cache directory to be inside the project directory since we can
+# only cache local items.
+variables:
+    PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+    VENV_CACHE_DIR: "$CI_PROJECT_DIR/venv"
+
+# Pip's cache doesn't store the python packages
+# https://pip.pypa.io/en/stable/reference/pip_install/#caching
+#
+# If you want to also cache the installed packages, you have to install
+# them in a virtualenv and cache it as well.
+cache:
+  paths:
+    - $PIP_CACHE_DIR
+    - $VENV_CACHE_DIR
+
+before_script:
+  - apt-get update
+  - apt-get install gcc gfortran build-essential wget libfreetype6-dev libpng-dev libopenblas-dev
+  - python -V
+  - pip install virtualenv
+  - virtualenv venv
+  - source venv/bin/activate
+
+stages:
+  - test
+
+test:
+  stage: test
+  script:
+    - python setup.py bdist_wheel
+    - pip uninstall -y neofox
+    - pip install dist/neofox-*.whl
+    - python -m unittest discover neofox.tests.unit_tests

INSTALL.md

@@ -0,0 +1,94 @@
+# Installation instructions
+
+This installation instructions were tested on Ubuntu 18.04.
+
+Python 3.7 and R 3.6.0 should be preinstalled.
+
+R requires the following libraries:
+```
+lattice
+ggplot2
+caret
+Peptides
+doParallel
+gbm
+```
+
+Set the environment variable pointing to `Rscript`.
+```
+export NEOFOX_RSCRIPT=`which Rscript`
+``` 
+
+## Install third-party dependencies
+
+### Install BLASTP
+
+The version of BLASTP that was tested is 2.8.1, other versions may work but that is untested.
+```
+wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.8.1/ncbi-blast-2.8.1+-x64-linux.tar.gz
+tar -xvf ncbi-blast-2.8.1+-x64-linux.tar.gz
+export NEOFOX_BLASTP=`pwd`/ncbi-blast-2.8.1+/bin/blastp
+```
+
+### Install NetMHCpan 4.0
+
+NetMHCpan 4.0 can be downloaded by academic users from https://services.healthtech.dtu.dk/service.php?NetMHCpan-4.0
+
+```
+tar -xvf netMHCpan-4.0a.Linux.tar.gz
+cd netMHCpan-4.0
+wget http://www.cbs.dtu.dk/services/NetMHCpan-4.0/data.Linux.tar.gz
+tar -xvf data.Linux.tar.gz
+cd ..
+export NEOFOX_NETMHCPAN=`pwd`/netMHCpan-4.0/netMHCpan
+```
+
+Configure NetMHCpan as explained in the file `netMHCpan-4.0/netMHCpan-4.0.readme`
+
+
+### Install NetMHC2pan 3.2
+
+NetMHC2pan can be downloaded by academic users from https://services.healthtech.dtu.dk/software.php
+
+```
+tar -xvf netMHCIIpan-3.2.Linux.tar.gz
+cd netMHCIIpan-3.2
+# download the data
+wget http://www.cbs.dtu.dk/services/NetMHCIIpan-3.2/data.Linux.tar.gz
+tar -xvf data.Linux.tar.gz
+cd ..
+export NEOFOX_NETMHC2PAN=`pwd`/netMHCIIpan-3.2/netMHCIIpan
+# install tcsh shell interpreter if not available yet
+sudo apt-get install tcsh
+```
+
+Configure NetMHCpan as explained in the file `netMHCIIpan-3.2/netMHCIIpan-3.2.readme`
+
+
+### Install MixMHCpred 2.0.1
+
+```
+wget https://github.com/GfellerLab/MixMHCpred/archive/v2.0.1.tar.gz
+tar -xvf v2.0.1.tar.gz
+export NEOFOX_MIXMHCPRED=`pwd`/MixMHCpred-2.0.1/MixMHCpred
+```
+
+Configure MixMHCpred as explained in the file `MixMHCpred-2.0.1/README`
+
+### Install MixMHC2pred 1.1.3
+
+```
+wget https://github.com/GfellerLab/MixMHC2pred/archive/v1.1.tar.gz
+tar -xvf v1.1.tar.gz
+export NEOFOX_MIXMHC2PRED=`pwd`/MixMHC2pred-1.1/MixMHC2pred_unix
+```
+
+## Install references
+
+For building the reference data we will need `makeblastdb`, set the environment variable required for building the reference:
+
+```
+export NEOFOX_MAKEBLASTDB=`pwd`/ncbi-blast-2.8.1+/bin/makeblastdb
+```
+
+Run the script in the neofox repository `neofox/references/build_references.sh` from your reference folder.