Tigmint 1.1.2

Basic information

  • Deploy date: 3 December 2019
  • Official Website: https://github.com/bcgsc/tigmint
  • License: GNU GPL v3
  • Installed on: Apolo II
  • Dependencies:
    • Miniconda 4.5.1 or greather
    • Bedtools
    • Bwa
    • Samtools
  • Optional dependencies:
    • Pigz. Recommended for parallel compression

Installation

  1. Before installing Tigmint install all its dependencies. After installing all the dependencies run:

    $ mkdir -p /share/apps/tigmint/1.1.2/miniconda/4.5.1
$ git clone https://github.com/bcgsc/tigmint
$ sudo cp -r tigmint/* /share/apps/tigmint/1.1.2/miniconda/4.5.1/

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

    1.1.2_miniconda-4.5.1
    #%Module1.0#####################################################################
##
## modulefile tigmint/1.1.2_miniconda-4.5.1
##
## Written by Hamilton Tobon Mosquera.
proc ModulesHelp { } {
     global version modroot
     puts stderr "\ttigmint - Sets the environment for using tigmint 1.1.2. \
     \nin the shared directory /share/apps/tigmint/1.1.2/miniconda/4.5.1."
}    

module-whatis "(Name________) tigmint"
module-whatis "(Version_____) 1.1.2 with Conda 4.5.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

set	      topdir	      /share/apps/tigmint/1.1.2/miniconda/4.5.1

conflict tigmint
module load python/3.6.5_miniconda-4.5.1
module load bwa/0.7.15_intel-2017_update-1
module load bedtools/2.26.0_intel-2017_update-1
module load samtools/1.3.1_intel-2017_update-1
module load pigz/2.4_intel-19.0.4

prepend-path	PATH		$topdir/bin

    Create the needed folder and place it:

    $ sudo mkdir /share/apps/modules/tigmint
$ sudo mv 1.1.2_miniconda-4.5.1 /share/apps/modules/tigmint/

Authors