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INSTALL.md

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CAARS

Dependencies tree

  • Transdecoder >= 3.0.1

  • FastTree >= 2.1.7 (Warning: The executable must be fasttree and not FastTree)

  • Python 2.7 (with pip and setuptools)

    • PyQt4
    • SciPy
    • MySQLdb
    • lxml
    • ete2
    • ete3
    • profileNJ
    • pandas
    • Biopython

  • Trinity >=2.3

    • Java >= 1.8 (OpenJRE works)
    • Bowtie >= 2 (tested with 2.2.9)

  • phyldog >= 1.1.0

    • libPLL >= 1.0.2 sequential
    • boost from 1.49 to 1.55 (versions >1.55 won't do for now)
    • bpp >= 2.2.0 (Bio++)

  • PhyloMerge (0.2 from 2017/01)

    • bpp >= 2.2.0 (Bio++)

  • apytram >= 1.0

    • exonerate >= 2.2.0
    • mafft >=7.1
    • blast+ >= 2.6
    • Seqtk >= 1.2
    • python = 2.7
    • cd-hit >= 4.6.6
    • Trinity >=2.3

  • OCaml >= 4.03.0

    • bistro = 0.3.0

dependencies installation via distribution packages

Like standard locations, or distribution packages.

Some (rare) dependencies may be installed via distribution packages. Example, on Debian based distributions:

apt-get install python-setuptools python-qt4 python-scipy python-mysqldb python-lxml python-pip fasttree exonerate mafft

You may need root rights (use for instance sudo)

Installation on non-standard locations

Here we describe a painfull, but complete, installation of CAARS and all its dependencies (out of order).

Python 2.7

With a site-packages on a non-standard location:

python -m easy_install --upgrade pip
python -m easy_install --upgrade setuptools
python -m easy_install --upgrade PyQt4
python -m easy_install --upgrade scipy
python -m easy_install --upgrade MySQLdb
python -m easy_install --upgrade lxml
python -m easy_install --upgrade ete2
python -m easy_install --upgrade ete3
python -m easy_install --upgrade profileNJ
python -m easy_install --upgrade pandas
python -m easy_install --upgrade matplotlib
python -m easy_install --upgrade biopython

Transdecoder >= 3.0.1

Get it from https://github.com/TransDecoder/TransDecoder. It's written in Perl, but it builds cd-hit.

mkdir -p /home/user/bin/TransDecoder
cd /home/user/bin/TransDecoder/
wget https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz
tar xvf v3.0.1.tar.gz
cd v3.0.1 && make

Add /home/user/bin/TransDecoder/v3.0.1 and /home/user/bin/TransDecoder/v3.0.1/util/bin to PATH.

FastTree >= 2.1.7

FastTree is distributed as binary. Get it from http://www.microbesonline.org/fasttree/.

mkdir -p /home/user/bin/FastTree/2.1.9/
cd /home/user/bin/FastTree/2.1.9/
wget http://www.microbesonline.org/fasttree/FastTree
ln -s FastTree fasttree

Add /home/user/bin/FastTree/2.1.9/ to PATH.

apytram >= 1.0

apytram is written in Python 2.7, but need following dependencies:

exonerate >= 2.2.0

exonerate is already packaged. See Dependencies installation via distribution packages.

mafft >=7.1

mafft is already packaged. See Dependencies installation via distribution packages.

blast+ >= 2.6

Blast+ is distributed as binary, which can be downloaded at the NCBI.

mkdir -p /home/user/bin/Blast/
wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz
tar zxf ncbi-blast-2.6.0+-x64-linux.tar.gz
mv blast-2.6.0+ 2.6.0+

Add /home/user/bin/Blast/2.6.0+/bin to PATH.

Seqtk >= 1.2

Toolkit for processing sequences in FASTA/Q formats https://github.com/lh3/seqtk

mkdir -p /home/user/bin/seqtk
git clone https://github.com/lh3/seqtk.git  /home/user/bin/seqtk
cd  /home/user/bin/seqtk
make

Add /home/user/bin/seqtk to PATH.

export PATH=/home/user/bin/seqtk:$PATH

CD-HIT >= 4.6.6

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences (http://weizhongli-lab.org/cd-hit/).

 git clone https://github.com/weizhongli/cdhit.git /home/user/bin/cdhit/
cd /home/user/bin/cdhit/cd-hit-auxtools
make
cd /home/user/bin/cdhit
make
make install

Add /home/user/bin/cd-hit-auxtools to PATH.

export PATH=/home/user/bin/cd-hit-auxtools:$PATH

Install apytram

git clone https://github.com/carinerey/apytram /home/user/bin/apytram

Add:

  • /home/user/bin/apytram to PATH.
  • /home/user/bin/apytram/ApytramLib to PYTHONPATH.

You can test if your apytram installation match all the requirements by using test_apytram_configuration.py, or by running make test into apytram directory (/home/user/bin/apytram). See apytram Wiki for more informations.

Trinity >=2.3

Trinity can be downloaded on github. You'll need to install first:

  • Java 1.8 (at least JRE 1.8u0)
  • Bowtie >= 2
Java >= 1.8

You can get Java from java.com.

mkdir -p /home/user/bin/java
cp jre-8u77-linux-x64.tar.gz /home/user/bin/java/
cd /home/user/bin/java/
tar --no-same-owner -xzvf jre-8u77-linux-x64.tar.gz

Add:

  • /home/user/bin/java/jre1.8.0_77 to JAVAHOME,
  • /home/user/bin/java/jre1.8.0_77/bin to PATH.
Bowtie >= 2

successfully tested with 2.2.9.

cd /home/user/bin/
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.0/bowtie2-2.3.0-source.zip
unzip bowtie2-2.3.0-source.zip
cd bowtie2-2.3.0/
make
make install

PhyloMerge (0.2 from 2017/01)

* bpp >= 2.2.0 (Bio++)

Bpp >= 2.2.0

Bio++ Program Suite (https://github.com/BioPP/bppsuite)

echo "deb http://biopp.univ-montp2.fr/repos/apt/ Trusty main" >> /etc/apt/sources.list;\
    wget http://biopp.univ-montp2.fr/repos/apt/conf/biopp.gpg.key
apt-key add biopp.gpg.key
apt-get update
apt-get install -qy libbpp-phyl-dev

Phylomerge

git clone https://github.com/boussau/phylomerge/ /home/user/bin/phylomerge
cd  /home/user/bin/phylomerge
bash ./compile

Add /home/user/bin/phylomerge to PATH.

export PATH=/home/user/bin/phylomerge:$PATH

phyldog:

* libPLL >= 1.0.2 sequential
* boost 1.55 < . > 1.49 (waiting for PSMN's validation on 1.63)
* bpp >= 2.2.0 (Bio++) (see above)

WARNING: phyldog, bpp, boost and mpi must be build with the same compiler.

libPLL >= 1.0.2

mkdir -p /home/user/lib/
cd /home/user/lib/
wget http://www.libpll.org/Downloads/libpll-1.0.2-sse3-64.tar.gz
tar xzf libpll-1.0.2-sse3-64.tar.gz && rm libpll-1.0.2-sse3-64.tar.gz
cd /home/user/lib/libpll-1.0.2-sse3-64/
cp libpll-sse3* /usr/local/lib
cp -r include/pll /usr/local/include/

Phyldog

cd /home/user/bin/
git clone https://github.com/Boussau/PHYLDOG phyldog

mkdir -p /home/user/bin/phyldog/build
cd /home/user/bin/phyldog/build


export LD_LIBRARY_PATH=/usr/local/lib/:$LD_LIBRARY_PATH  #(where you store libpll)

cmake ..
make
make install

OCaml

Get latest OCaml from http://ocaml.org/. Untar and build:

tar xvf ocaml-4.04.0.tar.gz
cd ocaml-4.04.0
./configure -prefix /home/user/binOCaml/4.04.0
make world
make bootstrap
make opt
su make install

Add:

  • /home/user/binOCaml/4.04.0/bin to PATH,
  • /home/user/binOCaml/4.04.0/lib to LD_LIBRARY_PATH,
  • /home/user/binOCaml/4.04.0/man to MANTPATH.

Use whatever-you-want environment tool :o) (as Module Environment, LMode, personnal rc files, etc.)

opam

  • Install opam (OCaml Package Manager):

See https://opam.ocaml.org/ for help.

wget https://raw.github.com/ocaml/opam/master/shell/opam_installer.sh
su ./opam_installer.sh /home/user/bin/OCaml/4.04.0/bin
  • Init opam

as user:

opam init
eval `opam config env`
  • Install CAARS OCaml depencies:

as user:

opam install -y bistro=0.3.0

CAARS

Finally (at last), install CAARS from github.

git clone https://github.com/carinerey/caars /home/user/bin/caars/
cd  /home/user/bin/caars/
make

Add /home/user/bin/caars/ to PATH. Add /home/user/bin/caars/utils/bin/ to PATH.

export PATH=/home/user/bin/caars/:$PATH

To test that all is okay, you can run make test

cd  /home/user/bin/caars/
make test