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Unverified Commit beac4302 authored by Laurent Modolo's avatar Laurent Modolo
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training_dataset.config: update CONDA_ENVS

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src/training_dataset.config
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......@@ -119,7 +119,7 @@ profiles {
process{
withName: build_synthetic_bed {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}bedtools_2.25.0"
conda = "$CONDA_ENVS/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
......@@ -129,7 +129,7 @@ profiles {
}
withName: fasta_from_bed {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}bedtools_2.25.0"
conda = "$CONDA_ENVS/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 1
......@@ -139,7 +139,7 @@ profiles {
}
withName: index_fasta {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -150,7 +150,7 @@ profiles {
}
withName: mapping_fastq_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -161,7 +161,7 @@ profiles {
}
withName: bam_2_fastq_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}samtools_1.7"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -172,7 +172,7 @@ profiles {
}
withName: sort_bam_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}samtools_1.7"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -183,7 +183,7 @@ profiles {
}
withName: index_bam_paired {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}samtools_1.7"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -194,7 +194,7 @@ profiles {
}
withName: mapping_fastq_single {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}bowtie2_2.3.4.1"
conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -205,7 +205,7 @@ profiles {
}
withName: bam_2_fastq_single {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}samtools_1.7"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -216,7 +216,7 @@ profiles {
}
withName: sort_bam_single {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}samtools_1.7"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......@@ -227,7 +227,7 @@ profiles {
}
withName: index_bam_single {
beforeScript = "./src/conda_psmn.sh"
conda = "${CONDA_ENVS}samtools_1.7"
conda = "$CONDA_ENVS/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
cpus = 16
......
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