Skip to content
Snippets Groups Projects
Unverified Commit 83c22dca authored by Laurent Modolo's avatar Laurent Modolo
Browse files

PSMN: add install script for conda modules

parent e58b21b6
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 145 additions and 60 deletions
src/conda_packages.sh
+ 145
− 60
View file @ 83c22dca
#!/bin/sh
function install_env {
if [ ! -d "${CONDA_PREFIX}/envs/${1}_${2}" ]; then
conda create --yes --name ${1}_${2} ${3}=${2}
fi
}
install_env pigz 2.3.4 pigz
install_env tophat 2.1.1 tophat
install_env hisat2 2.0.0 hisat2
install_env hisat2 2.1.0 hisat2
install_env rsem 1.3.1 rsem
install_env rsem 1.3.0 rsem
install_env samblaster 0.1.24 samblaster
install_env nextflow 0.25.1 nextflow
install_env nextflow 19.01.0 nextflow
install_env nextflow 0.32.0 nextflow
install_env nextflow 0.28.2 nextflow
install_env samtools 1.7 samtools
install_env samtools 1.5 samtools
install_env bowtie2 2.3.2 bowtie2
install_env bowtie2 2.3.4.1 bowtie2
install_env sratools 2.8.2 sra-tools
install_env trimmomatic 0.36 trimmomatic
install_env trimmomatic 0.39 trimmomatic
install_env Python 3.6.1 Python
install_env Python 2.7.13 Python
install_env kallisto 0.44.0 kallisto
install_env kallisto 0.43.1 kallisto
install_env music 1.0.0 music
install_env umitools 0.3.4 umitools
install_env umi_tools 1.0.0 umi_tools
install_env fastp 0.19.7 fastp
install_env gatk 3.8 gatk
install_env cutadapt 1.14 cutadapt
install_env cutadapt 2.1 cutadapt
install_env bioawk 1.0 bioawk
install_env canu 1.7 canu
install_env fastqc 0.11.5 fastqc
install_env bedtools 2.25.0 bedtools
install_env macs2 2.1.2 macs2
install_env bcftools 1.7 bcftools
install_env salmon 0.8.2 salmon
install_env urqt d62c1f8 urqt
install_env multiqc 0.9 multiqc
install_env multiqc 1.7 multiqc
install_env multiqc 1.0 multiqc
install_env cdhit 4.6.8 cdhit
install_env deeptools 3.0.2 deeptools
install_env htseq 0.9.1 htseq
install_env htseq 0.11.2 htseq
install_env python 3.7 python
install_env R 3.5.1 R
install_env R 3.4.3 R
install_env R 3.3.1 R
install_env file handle 0.1.1 file handle
install_env ncdu 1.13 ncdu
install_env picard 2.18.11 picard
install_env sambamba 0.6.7 sambamba
install_env subread 1.6.4 subread
source src/conda_psmn.sh
if [ ! -d ${CONDA_ENVS}pigz_2.3.4 ]; then
conda create --yes --name pigz_2.3.4 pigz=2.3.4
fi
if [ ! -d ${CONDA_ENVS}tophat_2.1.1 ]; then
conda create --yes --name tophat_2.1.1 tophat=2.1.1
fi
if [ ! -d ${CONDA_ENVS}hisat2_2.0.0 ]; then
conda create --yes --name hisat2_2.0.0 hisat2=2.0.0 samtools=1.7
fi
if [ ! -d ${CONDA_ENVS}hisat2_2.1.0 ]; then
conda create --yes --name hisat2_2.1.0 hisat2=2.1.0 samtools=1.7
fi
if [ ! -d ${CONDA_ENVS}rsem_1.3.1 ]; then
conda create --yes --name rsem_1.3.1 rsem=1.3.1 samtools=1.3
fi
if [ ! -d ${CONDA_ENVS}rsem_1.3.0 ]; then
conda create --yes --name rsem_1.3.0 rsem=1.3.0 samtools=1.3
fi
if [ ! -d ${CONDA_ENVS}samblaster_0.1.24 ]; then
conda create --yes --name samblaster_0.1.24 samblaster=0.1.24
fi
if [ ! -d ${CONDA_ENVS}nextflow_0.25.1 ]; then
conda create --yes --name nextflow_0.25.1 nextflow=0.25.1
fi
if [ ! -d ${CONDA_ENVS}nextflow_19.01.0 ]; then
conda create --yes --name nextflow_19.01.0 nextflow=19.01.0
fi
if [ ! -d ${CONDA_ENVS}nextflow_0.32.0 ]; then
conda create --yes --name nextflow_0.32.0 nextflow=0.32.0
fi
if [ ! -d ${CONDA_ENVS}nextflow_0.28.2 ]; then
conda create --yes --name nextflow_0.28.2 nextflow=0.28.2
fi
if [ ! -d ${CONDA_ENVS}samtools_1.7 ]; then
conda create --yes --name samtools_1.7 samtools=1.7
fi
if [ ! -d ${CONDA_ENVS}samtools_1.5 ]; then
conda create --yes --name samtools_1.5 samtools=1.5
fi
if [ ! -d ${CONDA_ENVS}bowtie2_2.3.2 ]; then
conda create --yes --name bowtie2_2.3.2 bowtie2=2.3.2 samtools=1.7
fi
if [ ! -d ${CONDA_ENVS}bowtie2_2.3.4.1 ]; then
conda create --yes --name bowtie2_2.3.4.1 bowtie2=2.3.4.1 samtools=1.7 #&& \
fi
if [ ! -d ${CONDA_ENVS}sra-tools_2.8.2 ]; then
conda create --yes --name sra-tools_2.8.2 sra-tools=2.8.2
fi
if [ ! -d ${CONDA_ENVS}trimmomatic_0.36 ]; then
conda create --yes --name trimmomatic_0.36 trimmomatic=0.36
fi
if [ ! -d ${CONDA_ENVS}trimmomatic_0.39 ]; then
conda create --yes --name trimmomatic_0.39 trimmomatic=0.39
fi
if [ ! -d ${CONDA_ENVS}Python_3.6.1 ]; then
conda create --yes --name Python_3.6.1 Python=3.6.1
fi
if [ ! -d ${CONDA_ENVS}Python_2.7.13 ]; then
conda create --yes --name Python_2.7.13 Python=2.7.13
fi
if [ ! -d ${CONDA_ENVS}kallisto_0.44.0 ]; then
conda create --yes --name kallisto_0.44.0 kallisto=0.44.0
fi
if [ ! -d ${CONDA_ENVS}kallisto_0.43.1 ]; then
conda create --yes --name kallisto_0.43.1 kallisto=0.43.1
fi
if [ ! -d ${CONDA_ENVS}music_1.0.0 ]; then
conda create --yes --name music_1.0.0 music=1.0.0
fi
if [ ! -d ${CONDA_ENVS}umitools_0.3.4 ]; then
conda create --yes --name umitools_0.3.4 umitools=0.3.4
fi
if [ ! -d ${CONDA_ENVS}fastp_0.19.7 ]; then
conda create --yes --name fastp_0.19.7 fastp=0.19.7
fi
if [ ! -d ${CONDA_ENVS}gatk_3.8 ]; then
conda create --yes --name gatk_3.8 gatk=3.8
fi
if [ ! -d ${CONDA_ENVS}cutadapt_1.14 ]; then
conda create --yes --name cutadapt_1.14 cutadapt=1.14
fi
if [ ! -d ${CONDA_ENVS}bioawk_1.0 ]; then
conda create --yes --name bioawk_1.0 bioawk=1.0
fi
if [ ! -d ${CONDA_ENVS}canu_1.7 ]; then
conda create --yes --name canu_1.7 canu=1.7
fi
if [ ! -d ${CONDA_ENVS}fastqc_0.11.5 ]; then
conda create --yes --name fastqc_0.11.5 fastqc=0.11.5
fi
if [ ! -d ${CONDA_ENVS}bedtools_2.25.0 ]; then
conda create --yes --name bedtools_2.25.0 bedtools=2.25.0
fi
if [ ! -d ${CONDA_ENVS}macs2_2.1.2 ]; then
conda create --yes --name macs2_2.1.2 macs2=2.1.2
fi
if [ ! -d ${CONDA_ENVS}bcftools_1.7 ]; then
conda create --yes --name bcftools_1.7 bcftools=1.7
fi
if [ ! -d ${CONDA_ENVS}salmon_0.8.2 ]; then
conda create --yes --name salmon_0.8.2 salmon=0.8.2
fi
if [ ! -d ${CONDA_ENVS}urqt_d62c1f8 ]; then
conda create --yes --name urqt_d62c1f8 urqt=d62c1f8
fi
if [ ! -d ${CONDA_ENVS}multiqc_0.9 ]; then
conda create --yes --name multiqc_0.9 multiqc=0.9
fi
if [ ! -d ${CONDA_ENVS}multiqc_1.7 ]; then
conda create --yes --name multiqc_1.7 multiqc=1.7
fi
if [ ! -d ${CONDA_ENVS}multiqc_1.0 ]; then
conda create --yes --name multiqc_1.0 multiqc=1.0
fi
if [ ! -d ${CONDA_ENVS}cdhit_4.6.8 ]; then
conda create --yes --name cdhit_4.6.8 cdhit=4.6.8
fi
if [ ! -d ${CONDA_ENVS}deeptools_3.0.2 ]; then
conda create --yes --name deeptools_3.0.2 deeptools=3.0.2
fi
if [ ! -d ${CONDA_ENVS}htseq_0.9.1 ]; then
conda create --yes --name htseq_0.9.1 htseq=0.9.1
fi
if [ ! -d ${CONDA_ENVS}htseq_0.11.2 ]; then
conda create --yes --name htseq_0.11.2 htseq=0.11.2
fi
if [ ! -d ${CONDA_ENVS}R_3.4.3 ]; then
conda create --yes --name R_3.4.3 R=3.4.3
fi
if [ ! -d ${CONDA_ENVS}R_3.3.1 ]; then
conda create --yes --name R_3.3.1 R=3.3.1
fi
if [ ! -d ${CONDA_ENVS}file_handle_0.1.1 ]; then
conda create --yes --name file_handle_0.1.1 file_handle=0.1.1
fi
if [ ! -d ${CONDA_ENVS}ncdu_1.13 ]; then
conda create --yes --name ncdu_1.13 ncdu=1.13
fi
if [ ! -d ${CONDA_ENVS}picard_2.18.11 ]; then
conda create --yes --name picard_2.18.11 picard=2.18.11
fi
if [ ! -d ${CONDA_ENVS}sambamba_0.6.7 ]; then
conda create --yes --name sambamba_0.6.7 sambamba=0.6.7
fi
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment