Trans-ABySS 2.0.1

Basic information

Installation

  1. Before installing Trans-ABySS install ABySS and BLAT. Then run:

    $ module load python/3.6.5_miniconda-4.5.1

# Instead of "biology" any name can be used.
$ conda create -n biology python=3.7
$ conda activate biology
$ pip install python-igraph

    Test:

    $ module load blat/36_intel-19.0.4
$ module load abyss/2.2.3_gcc-5.4.0
$ git clone https://github.com/bcgsc/transabyss.git
$ cd transabyss
$ bash sample_dataset/assemble.sh
$ rm -rf sample_dataset/merged.fa  sample_dataset/test.k25  sample_dataset/test.k32

    Install the scripts. From the Trans-ABySS’ directory:

    $ sudo mkdir -p /share/apps/transabyss/2.0.1/miniconda-4.5.1
$ sudo cp -r * /share/apps/transabyss/2.0.1/miniconda-4.5.1/*

  2. Create and place the needed module file. Create a file with the following content:

    2.0.1_miniconda-4.5.1
    #%Module1.0####################################################################
##
## module load transabyss/2018
##
## /share/apps/modules/transabyss/2018
## Written by Hamilton Tobon Mosquera.
##

proc ModulesHelp {} {
         global version modroot
         puts stderr "Sets the environment for using Trans-AByss 2018 update \
         \nin the shared directory \
         \n/share/apps/transabyss/2.0.1/miniconda-4.5.1"
}

module-whatis "(Name________) transabyss"
module-whatis "(Version_____) 2.0.1 Miniconda 4.5.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/transabyss/2.0.1/miniconda-4.5.1
set         version       2.0.1
set         sys           x86_64-redhat-linux

conflict transabyss
module load blat/36_intel-19.0.4
module load abyss/2.2.3_gcc-5.4.0

prepend-path   PATH            $topdir
prepend-path   PATH            $topdir/bin

    Create the needed folder and place it:

    $ sudo mkdir /share/apps/modules/transabyss
$ sudo mv 2.0.1_miniconda-4.5.1 /share/apps/modules/transabyss/

Usage

Always activate the conda environment where python-igraph was installed, in this case:

conda activate biology

Authors