From 3e09b51392899d5c68399aa0c8b377c08f119af5 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 15:21:56 +0200
Subject: [PATCH] rm old script from src/
---
src/.conda_envs/.conda_envs_dir_test | 1 -
src/.conda_envs/Python_2.7.13 | 1 -
src/.conda_envs/Python_3.6.1 | 1 -
src/.conda_envs/R_3.3.1 | 1 -
src/.conda_envs/R_3.4.3 | 1 -
src/.conda_envs/axtchain_377 | 1 -
src/.conda_envs/bcftools_1.7 | 1 -
src/.conda_envs/bedtools_2.25.0 | 1 -
src/.conda_envs/bioawk_1.0 | 1 -
src/.conda_envs/biopython_1.74 | 1 -
src/.conda_envs/bowtie2_2.3.2 | 1 -
src/.conda_envs/bowtie2_2.3.4.1 | 1 -
src/.conda_envs/bwa_0.7.17 | 1 -
src/.conda_envs/canu_1.7 | 1 -
src/.conda_envs/cdhit_4.6.8 | 1 -
src/.conda_envs/cutadapt_1.14 | 1 -
src/.conda_envs/cutadapt_2.4 | 1 -
src/.conda_envs/deeptools_3.0.2 | 1 -
src/.conda_envs/envs | 1 -
src/.conda_envs/fastp_0.19.7 | 1 -
src/.conda_envs/fastqc_0.11.5 | 1 -
src/.conda_envs/flexi-splitter_1.0.0 | 1 -
src/.conda_envs/gatk_3.8 | 1 -
src/.conda_envs/gatk_3.8.0 | 1 -
src/.conda_envs/gatk_4.0.8.1 | 1 -
src/.conda_envs/hisat2_2.0.0 | 1 -
src/.conda_envs/hisat2_2.1.0 | 1 -
src/.conda_envs/htseq_0.11.2 | 1 -
src/.conda_envs/htseq_0.9.1 | 1 -
src/.conda_envs/kallisto_0.43.1 | 1 -
src/.conda_envs/kallisto_0.44.0 | 1 -
src/.conda_envs/last_1060 | 1 -
src/.conda_envs/liftover_357 | 1 -
src/.conda_envs/macs2_2.1.2 | 1 -
src/.conda_envs/multiqc_0.9 | 1 -
src/.conda_envs/multiqc_1.0 | 1 -
src/.conda_envs/multiqc_1.7 | 1 -
src/.conda_envs/music_1.0.0 | 1 -
src/.conda_envs/ncdu | 1 -
src/.conda_envs/nextflow_0.25.1 | 1 -
src/.conda_envs/nextflow_0.28.2 | 1 -
src/.conda_envs/nextflow_0.32.0 | 1 -
src/.conda_envs/nextflow_19.01.0 | 1 -
src/.conda_envs/picard_2.18.11 | 1 -
src/.conda_envs/pigz_2.3.4 | 1 -
src/.conda_envs/prinseq_0.20.4 | 1 -
src/.conda_envs/python_mars_seq_modules | 1 -
src/.conda_envs/r_mars_seq_modules_r | 1 -
src/.conda_envs/ribotish_0.2.4 | 1 -
src/.conda_envs/rsem_1.3.0 | 1 -
src/.conda_envs/rsem_1.3.1 | 1 -
src/.conda_envs/salmon_0.8.2 | 1 -
src/.conda_envs/samblaster_0.1.24 | 1 -
src/.conda_envs/samtools_1.5 | 1 -
src/.conda_envs/samtools_1.7 | 1 -
src/.conda_envs/seaborn_0.9.0 | 1 -
src/.conda_envs/splicing_lore_env | 1 -
src/.conda_envs/sra-tools_2.8.2 | 1 -
src/.conda_envs/star_2.5.3a | 1 -
src/.conda_envs/star_2.7.0e | 1 -
src/.conda_envs/star_2.7.3a | 1 -
src/.conda_envs/subread_1.6.4 | 1 -
src/.conda_envs/tophat_2.1.1 | 1 -
src/.conda_envs/trimmomatic_0.36 | 1 -
src/.conda_envs/trimmomatic_0.39 | 1 -
src/.conda_envs/ucsc_375 | 1 -
src/.conda_envs/umitools_0.3.4 | 1 -
src/.conda_envs/urqt_d62c1f8 | 1 -
src/.conda_packages.sh | 164 ------------------------
src/.conda_psmn.sh | 1 -
src/.update_config.sh | 32 -----
src/.update_tools.sh | 92 -------------
72 files changed, 357 deletions(-)
delete mode 120000 src/.conda_envs/.conda_envs_dir_test
delete mode 120000 src/.conda_envs/Python_2.7.13
delete mode 120000 src/.conda_envs/Python_3.6.1
delete mode 120000 src/.conda_envs/R_3.3.1
delete mode 120000 src/.conda_envs/R_3.4.3
delete mode 120000 src/.conda_envs/axtchain_377
delete mode 120000 src/.conda_envs/bcftools_1.7
delete mode 120000 src/.conda_envs/bedtools_2.25.0
delete mode 120000 src/.conda_envs/bioawk_1.0
delete mode 120000 src/.conda_envs/biopython_1.74
delete mode 120000 src/.conda_envs/bowtie2_2.3.2
delete mode 120000 src/.conda_envs/bowtie2_2.3.4.1
delete mode 120000 src/.conda_envs/bwa_0.7.17
delete mode 120000 src/.conda_envs/canu_1.7
delete mode 120000 src/.conda_envs/cdhit_4.6.8
delete mode 120000 src/.conda_envs/cutadapt_1.14
delete mode 120000 src/.conda_envs/cutadapt_2.4
delete mode 120000 src/.conda_envs/deeptools_3.0.2
delete mode 120000 src/.conda_envs/envs
delete mode 120000 src/.conda_envs/fastp_0.19.7
delete mode 120000 src/.conda_envs/fastqc_0.11.5
delete mode 120000 src/.conda_envs/flexi-splitter_1.0.0
delete mode 120000 src/.conda_envs/gatk_3.8
delete mode 120000 src/.conda_envs/gatk_3.8.0
delete mode 120000 src/.conda_envs/gatk_4.0.8.1
delete mode 120000 src/.conda_envs/hisat2_2.0.0
delete mode 120000 src/.conda_envs/hisat2_2.1.0
delete mode 120000 src/.conda_envs/htseq_0.11.2
delete mode 120000 src/.conda_envs/htseq_0.9.1
delete mode 120000 src/.conda_envs/kallisto_0.43.1
delete mode 120000 src/.conda_envs/kallisto_0.44.0
delete mode 120000 src/.conda_envs/last_1060
delete mode 120000 src/.conda_envs/liftover_357
delete mode 120000 src/.conda_envs/macs2_2.1.2
delete mode 120000 src/.conda_envs/multiqc_0.9
delete mode 120000 src/.conda_envs/multiqc_1.0
delete mode 120000 src/.conda_envs/multiqc_1.7
delete mode 120000 src/.conda_envs/music_1.0.0
delete mode 120000 src/.conda_envs/ncdu
delete mode 120000 src/.conda_envs/nextflow_0.25.1
delete mode 120000 src/.conda_envs/nextflow_0.28.2
delete mode 120000 src/.conda_envs/nextflow_0.32.0
delete mode 120000 src/.conda_envs/nextflow_19.01.0
delete mode 120000 src/.conda_envs/picard_2.18.11
delete mode 120000 src/.conda_envs/pigz_2.3.4
delete mode 120000 src/.conda_envs/prinseq_0.20.4
delete mode 120000 src/.conda_envs/python_mars_seq_modules
delete mode 120000 src/.conda_envs/r_mars_seq_modules_r
delete mode 120000 src/.conda_envs/ribotish_0.2.4
delete mode 120000 src/.conda_envs/rsem_1.3.0
delete mode 120000 src/.conda_envs/rsem_1.3.1
delete mode 120000 src/.conda_envs/salmon_0.8.2
delete mode 120000 src/.conda_envs/samblaster_0.1.24
delete mode 120000 src/.conda_envs/samtools_1.5
delete mode 120000 src/.conda_envs/samtools_1.7
delete mode 120000 src/.conda_envs/seaborn_0.9.0
delete mode 120000 src/.conda_envs/splicing_lore_env
delete mode 120000 src/.conda_envs/sra-tools_2.8.2
delete mode 120000 src/.conda_envs/star_2.5.3a
delete mode 120000 src/.conda_envs/star_2.7.0e
delete mode 120000 src/.conda_envs/star_2.7.3a
delete mode 120000 src/.conda_envs/subread_1.6.4
delete mode 120000 src/.conda_envs/tophat_2.1.1
delete mode 120000 src/.conda_envs/trimmomatic_0.36
delete mode 120000 src/.conda_envs/trimmomatic_0.39
delete mode 120000 src/.conda_envs/ucsc_375
delete mode 120000 src/.conda_envs/umitools_0.3.4
delete mode 120000 src/.conda_envs/urqt_d62c1f8
delete mode 100644 src/.conda_packages.sh
delete mode 120000 src/.conda_psmn.sh
delete mode 100644 src/.update_config.sh
delete mode 100755 src/.update_tools.sh
diff --git a/src/.conda_envs/.conda_envs_dir_test b/src/.conda_envs/.conda_envs_dir_test
deleted file mode 120000
index 79b89f16..00000000
--- a/src/.conda_envs/.conda_envs_dir_test
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/.conda_envs_dir_test
\ No newline at end of file
diff --git a/src/.conda_envs/Python_2.7.13 b/src/.conda_envs/Python_2.7.13
deleted file mode 120000
index 5c91793f..00000000
--- a/src/.conda_envs/Python_2.7.13
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/Python_2.7.13
\ No newline at end of file
diff --git a/src/.conda_envs/Python_3.6.1 b/src/.conda_envs/Python_3.6.1
deleted file mode 120000
index 7a6e74cf..00000000
--- a/src/.conda_envs/Python_3.6.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/Python_3.6.1
\ No newline at end of file
diff --git a/src/.conda_envs/R_3.3.1 b/src/.conda_envs/R_3.3.1
deleted file mode 120000
index 6544e090..00000000
--- a/src/.conda_envs/R_3.3.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/R_3.3.1
\ No newline at end of file
diff --git a/src/.conda_envs/R_3.4.3 b/src/.conda_envs/R_3.4.3
deleted file mode 120000
index 2f455802..00000000
--- a/src/.conda_envs/R_3.4.3
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/R_3.4.3
\ No newline at end of file
diff --git a/src/.conda_envs/axtchain_377 b/src/.conda_envs/axtchain_377
deleted file mode 120000
index 845b1a93..00000000
--- a/src/.conda_envs/axtchain_377
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/axtchain_377
\ No newline at end of file
diff --git a/src/.conda_envs/bcftools_1.7 b/src/.conda_envs/bcftools_1.7
deleted file mode 120000
index c77cd622..00000000
--- a/src/.conda_envs/bcftools_1.7
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/bcftools_1.7
\ No newline at end of file
diff --git a/src/.conda_envs/bedtools_2.25.0 b/src/.conda_envs/bedtools_2.25.0
deleted file mode 120000
index da8bc774..00000000
--- a/src/.conda_envs/bedtools_2.25.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/bedtools_2.25.0
\ No newline at end of file
diff --git a/src/.conda_envs/bioawk_1.0 b/src/.conda_envs/bioawk_1.0
deleted file mode 120000
index 1907adb0..00000000
--- a/src/.conda_envs/bioawk_1.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/bioawk_1.0
\ No newline at end of file
diff --git a/src/.conda_envs/biopython_1.74 b/src/.conda_envs/biopython_1.74
deleted file mode 120000
index a32165ca..00000000
--- a/src/.conda_envs/biopython_1.74
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/biopython_1.74
\ No newline at end of file
diff --git a/src/.conda_envs/bowtie2_2.3.2 b/src/.conda_envs/bowtie2_2.3.2
deleted file mode 120000
index 6f58283d..00000000
--- a/src/.conda_envs/bowtie2_2.3.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/bowtie2_2.3.2
\ No newline at end of file
diff --git a/src/.conda_envs/bowtie2_2.3.4.1 b/src/.conda_envs/bowtie2_2.3.4.1
deleted file mode 120000
index ee79b396..00000000
--- a/src/.conda_envs/bowtie2_2.3.4.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/bowtie2_2.3.4.1
\ No newline at end of file
diff --git a/src/.conda_envs/bwa_0.7.17 b/src/.conda_envs/bwa_0.7.17
deleted file mode 120000
index 8ee9986b..00000000
--- a/src/.conda_envs/bwa_0.7.17
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/bwa_0.7.17
\ No newline at end of file
diff --git a/src/.conda_envs/canu_1.7 b/src/.conda_envs/canu_1.7
deleted file mode 120000
index 3b3b783c..00000000
--- a/src/.conda_envs/canu_1.7
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/canu_1.7
\ No newline at end of file
diff --git a/src/.conda_envs/cdhit_4.6.8 b/src/.conda_envs/cdhit_4.6.8
deleted file mode 120000
index 0250dfbb..00000000
--- a/src/.conda_envs/cdhit_4.6.8
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/cdhit_4.6.8
\ No newline at end of file
diff --git a/src/.conda_envs/cutadapt_1.14 b/src/.conda_envs/cutadapt_1.14
deleted file mode 120000
index 33552e9c..00000000
--- a/src/.conda_envs/cutadapt_1.14
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/cutadapt_1.14
\ No newline at end of file
diff --git a/src/.conda_envs/cutadapt_2.4 b/src/.conda_envs/cutadapt_2.4
deleted file mode 120000
index c2ab68ca..00000000
--- a/src/.conda_envs/cutadapt_2.4
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/cutadapt_2.4
\ No newline at end of file
diff --git a/src/.conda_envs/deeptools_3.0.2 b/src/.conda_envs/deeptools_3.0.2
deleted file mode 120000
index 514f9cd8..00000000
--- a/src/.conda_envs/deeptools_3.0.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/deeptools_3.0.2
\ No newline at end of file
diff --git a/src/.conda_envs/envs b/src/.conda_envs/envs
deleted file mode 120000
index cf88bffb..00000000
--- a/src/.conda_envs/envs
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/
\ No newline at end of file
diff --git a/src/.conda_envs/fastp_0.19.7 b/src/.conda_envs/fastp_0.19.7
deleted file mode 120000
index 325a0da0..00000000
--- a/src/.conda_envs/fastp_0.19.7
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/fastp_0.19.7
\ No newline at end of file
diff --git a/src/.conda_envs/fastqc_0.11.5 b/src/.conda_envs/fastqc_0.11.5
deleted file mode 120000
index 73298f6f..00000000
--- a/src/.conda_envs/fastqc_0.11.5
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/fastqc_0.11.5
\ No newline at end of file
diff --git a/src/.conda_envs/flexi-splitter_1.0.0 b/src/.conda_envs/flexi-splitter_1.0.0
deleted file mode 120000
index 48e58235..00000000
--- a/src/.conda_envs/flexi-splitter_1.0.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/flexi-splitter_1.0.0
\ No newline at end of file
diff --git a/src/.conda_envs/gatk_3.8 b/src/.conda_envs/gatk_3.8
deleted file mode 120000
index 63462f44..00000000
--- a/src/.conda_envs/gatk_3.8
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/gatk_3.8
\ No newline at end of file
diff --git a/src/.conda_envs/gatk_3.8.0 b/src/.conda_envs/gatk_3.8.0
deleted file mode 120000
index 0463b9cc..00000000
--- a/src/.conda_envs/gatk_3.8.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/gatk_3.8.0
\ No newline at end of file
diff --git a/src/.conda_envs/gatk_4.0.8.1 b/src/.conda_envs/gatk_4.0.8.1
deleted file mode 120000
index 96fb8371..00000000
--- a/src/.conda_envs/gatk_4.0.8.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/gatk_4.0.8.1
\ No newline at end of file
diff --git a/src/.conda_envs/hisat2_2.0.0 b/src/.conda_envs/hisat2_2.0.0
deleted file mode 120000
index 31d43002..00000000
--- a/src/.conda_envs/hisat2_2.0.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/hisat2_2.0.0
\ No newline at end of file
diff --git a/src/.conda_envs/hisat2_2.1.0 b/src/.conda_envs/hisat2_2.1.0
deleted file mode 120000
index 2a26ea5b..00000000
--- a/src/.conda_envs/hisat2_2.1.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/hisat2_2.1.0
\ No newline at end of file
diff --git a/src/.conda_envs/htseq_0.11.2 b/src/.conda_envs/htseq_0.11.2
deleted file mode 120000
index 512c5ab4..00000000
--- a/src/.conda_envs/htseq_0.11.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/htseq_0.11.2
\ No newline at end of file
diff --git a/src/.conda_envs/htseq_0.9.1 b/src/.conda_envs/htseq_0.9.1
deleted file mode 120000
index a0b11c0b..00000000
--- a/src/.conda_envs/htseq_0.9.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/htseq_0.9.1
\ No newline at end of file
diff --git a/src/.conda_envs/kallisto_0.43.1 b/src/.conda_envs/kallisto_0.43.1
deleted file mode 120000
index f97de91a..00000000
--- a/src/.conda_envs/kallisto_0.43.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/kallisto_0.43.1
\ No newline at end of file
diff --git a/src/.conda_envs/kallisto_0.44.0 b/src/.conda_envs/kallisto_0.44.0
deleted file mode 120000
index 63b3d7d5..00000000
--- a/src/.conda_envs/kallisto_0.44.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/kallisto_0.44.0
\ No newline at end of file
diff --git a/src/.conda_envs/last_1060 b/src/.conda_envs/last_1060
deleted file mode 120000
index 2015c985..00000000
--- a/src/.conda_envs/last_1060
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/last_1060
\ No newline at end of file
diff --git a/src/.conda_envs/liftover_357 b/src/.conda_envs/liftover_357
deleted file mode 120000
index ba72fec9..00000000
--- a/src/.conda_envs/liftover_357
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/liftover_357
\ No newline at end of file
diff --git a/src/.conda_envs/macs2_2.1.2 b/src/.conda_envs/macs2_2.1.2
deleted file mode 120000
index d14a7fd7..00000000
--- a/src/.conda_envs/macs2_2.1.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/macs2_2.1.2
\ No newline at end of file
diff --git a/src/.conda_envs/multiqc_0.9 b/src/.conda_envs/multiqc_0.9
deleted file mode 120000
index 57372d0c..00000000
--- a/src/.conda_envs/multiqc_0.9
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/multiqc_0.9
\ No newline at end of file
diff --git a/src/.conda_envs/multiqc_1.0 b/src/.conda_envs/multiqc_1.0
deleted file mode 120000
index db90e686..00000000
--- a/src/.conda_envs/multiqc_1.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/multiqc_1.0
\ No newline at end of file
diff --git a/src/.conda_envs/multiqc_1.7 b/src/.conda_envs/multiqc_1.7
deleted file mode 120000
index 46bbaff8..00000000
--- a/src/.conda_envs/multiqc_1.7
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/multiqc_1.7
\ No newline at end of file
diff --git a/src/.conda_envs/music_1.0.0 b/src/.conda_envs/music_1.0.0
deleted file mode 120000
index c451a47d..00000000
--- a/src/.conda_envs/music_1.0.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/music_1.0.0
\ No newline at end of file
diff --git a/src/.conda_envs/ncdu b/src/.conda_envs/ncdu
deleted file mode 120000
index f46dbc26..00000000
--- a/src/.conda_envs/ncdu
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/ncdu
\ No newline at end of file
diff --git a/src/.conda_envs/nextflow_0.25.1 b/src/.conda_envs/nextflow_0.25.1
deleted file mode 120000
index b419d0ba..00000000
--- a/src/.conda_envs/nextflow_0.25.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/nextflow_0.25.1
\ No newline at end of file
diff --git a/src/.conda_envs/nextflow_0.28.2 b/src/.conda_envs/nextflow_0.28.2
deleted file mode 120000
index d6f5f3dc..00000000
--- a/src/.conda_envs/nextflow_0.28.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/nextflow_0.28.2
\ No newline at end of file
diff --git a/src/.conda_envs/nextflow_0.32.0 b/src/.conda_envs/nextflow_0.32.0
deleted file mode 120000
index 439a1521..00000000
--- a/src/.conda_envs/nextflow_0.32.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/nextflow_0.32.0
\ No newline at end of file
diff --git a/src/.conda_envs/nextflow_19.01.0 b/src/.conda_envs/nextflow_19.01.0
deleted file mode 120000
index 18a20221..00000000
--- a/src/.conda_envs/nextflow_19.01.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/nextflow_19.01.0
\ No newline at end of file
diff --git a/src/.conda_envs/picard_2.18.11 b/src/.conda_envs/picard_2.18.11
deleted file mode 120000
index cbf205fe..00000000
--- a/src/.conda_envs/picard_2.18.11
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/picard_2.18.11
\ No newline at end of file
diff --git a/src/.conda_envs/pigz_2.3.4 b/src/.conda_envs/pigz_2.3.4
deleted file mode 120000
index 33455f84..00000000
--- a/src/.conda_envs/pigz_2.3.4
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/pigz_2.3.4
\ No newline at end of file
diff --git a/src/.conda_envs/prinseq_0.20.4 b/src/.conda_envs/prinseq_0.20.4
deleted file mode 120000
index dca20610..00000000
--- a/src/.conda_envs/prinseq_0.20.4
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/prinseq_0.20.4
\ No newline at end of file
diff --git a/src/.conda_envs/python_mars_seq_modules b/src/.conda_envs/python_mars_seq_modules
deleted file mode 120000
index cd3910ea..00000000
--- a/src/.conda_envs/python_mars_seq_modules
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/python_mars_seq_modules
\ No newline at end of file
diff --git a/src/.conda_envs/r_mars_seq_modules_r b/src/.conda_envs/r_mars_seq_modules_r
deleted file mode 120000
index 00ebf61d..00000000
--- a/src/.conda_envs/r_mars_seq_modules_r
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/r_mars_seq_modules_r
\ No newline at end of file
diff --git a/src/.conda_envs/ribotish_0.2.4 b/src/.conda_envs/ribotish_0.2.4
deleted file mode 120000
index 173ef748..00000000
--- a/src/.conda_envs/ribotish_0.2.4
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/ribotish_0.2.4
\ No newline at end of file
diff --git a/src/.conda_envs/rsem_1.3.0 b/src/.conda_envs/rsem_1.3.0
deleted file mode 120000
index cea23372..00000000
--- a/src/.conda_envs/rsem_1.3.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/rsem_1.3.0
\ No newline at end of file
diff --git a/src/.conda_envs/rsem_1.3.1 b/src/.conda_envs/rsem_1.3.1
deleted file mode 120000
index 325fb238..00000000
--- a/src/.conda_envs/rsem_1.3.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/rsem_1.3.1
\ No newline at end of file
diff --git a/src/.conda_envs/salmon_0.8.2 b/src/.conda_envs/salmon_0.8.2
deleted file mode 120000
index 65b04e4b..00000000
--- a/src/.conda_envs/salmon_0.8.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/salmon_0.8.2
\ No newline at end of file
diff --git a/src/.conda_envs/samblaster_0.1.24 b/src/.conda_envs/samblaster_0.1.24
deleted file mode 120000
index d0093267..00000000
--- a/src/.conda_envs/samblaster_0.1.24
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/samblaster_0.1.24
\ No newline at end of file
diff --git a/src/.conda_envs/samtools_1.5 b/src/.conda_envs/samtools_1.5
deleted file mode 120000
index cab31c46..00000000
--- a/src/.conda_envs/samtools_1.5
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/samtools_1.5
\ No newline at end of file
diff --git a/src/.conda_envs/samtools_1.7 b/src/.conda_envs/samtools_1.7
deleted file mode 120000
index 29a7fb1e..00000000
--- a/src/.conda_envs/samtools_1.7
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/samtools_1.7
\ No newline at end of file
diff --git a/src/.conda_envs/seaborn_0.9.0 b/src/.conda_envs/seaborn_0.9.0
deleted file mode 120000
index dedf18f4..00000000
--- a/src/.conda_envs/seaborn_0.9.0
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/seaborn_0.9.0
\ No newline at end of file
diff --git a/src/.conda_envs/splicing_lore_env b/src/.conda_envs/splicing_lore_env
deleted file mode 120000
index f5570a06..00000000
--- a/src/.conda_envs/splicing_lore_env
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/splicing_lore_env
\ No newline at end of file
diff --git a/src/.conda_envs/sra-tools_2.8.2 b/src/.conda_envs/sra-tools_2.8.2
deleted file mode 120000
index a01645bc..00000000
--- a/src/.conda_envs/sra-tools_2.8.2
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/sra-tools_2.8.2
\ No newline at end of file
diff --git a/src/.conda_envs/star_2.5.3a b/src/.conda_envs/star_2.5.3a
deleted file mode 120000
index 6030edb0..00000000
--- a/src/.conda_envs/star_2.5.3a
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/star_2.5.3a
\ No newline at end of file
diff --git a/src/.conda_envs/star_2.7.0e b/src/.conda_envs/star_2.7.0e
deleted file mode 120000
index b8cafd08..00000000
--- a/src/.conda_envs/star_2.7.0e
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/star_2.7.0e
\ No newline at end of file
diff --git a/src/.conda_envs/star_2.7.3a b/src/.conda_envs/star_2.7.3a
deleted file mode 120000
index c25c3a3c..00000000
--- a/src/.conda_envs/star_2.7.3a
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/star_2.7.3a
\ No newline at end of file
diff --git a/src/.conda_envs/subread_1.6.4 b/src/.conda_envs/subread_1.6.4
deleted file mode 120000
index e7bba79d..00000000
--- a/src/.conda_envs/subread_1.6.4
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/subread_1.6.4
\ No newline at end of file
diff --git a/src/.conda_envs/tophat_2.1.1 b/src/.conda_envs/tophat_2.1.1
deleted file mode 120000
index 6bb53f91..00000000
--- a/src/.conda_envs/tophat_2.1.1
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/tophat_2.1.1
\ No newline at end of file
diff --git a/src/.conda_envs/trimmomatic_0.36 b/src/.conda_envs/trimmomatic_0.36
deleted file mode 120000
index 77753a1c..00000000
--- a/src/.conda_envs/trimmomatic_0.36
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/trimmomatic_0.36
\ No newline at end of file
diff --git a/src/.conda_envs/trimmomatic_0.39 b/src/.conda_envs/trimmomatic_0.39
deleted file mode 120000
index 81502468..00000000
--- a/src/.conda_envs/trimmomatic_0.39
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/trimmomatic_0.39
\ No newline at end of file
diff --git a/src/.conda_envs/ucsc_375 b/src/.conda_envs/ucsc_375
deleted file mode 120000
index 406934cb..00000000
--- a/src/.conda_envs/ucsc_375
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/ucsc_375
\ No newline at end of file
diff --git a/src/.conda_envs/umitools_0.3.4 b/src/.conda_envs/umitools_0.3.4
deleted file mode 120000
index 1fbf3fc6..00000000
--- a/src/.conda_envs/umitools_0.3.4
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/umitools_0.3.4
\ No newline at end of file
diff --git a/src/.conda_envs/urqt_d62c1f8 b/src/.conda_envs/urqt_d62c1f8
deleted file mode 120000
index bb665c60..00000000
--- a/src/.conda_envs/urqt_d62c1f8
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/envs/urqt_d62c1f8
\ No newline at end of file
diff --git a/src/.conda_packages.sh b/src/.conda_packages.sh
deleted file mode 100644
index 86b2575c..00000000
--- a/src/.conda_packages.sh
+++ /dev/null
@@ -1,164 +0,0 @@
-source src/.conda_psmn.sh
-CONDA_ENVS=src/.conda_envs/
-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}bwa_0.7.17 ]; then
- conda create --yes --name bwa_0.7.17 -c bioconda bwa=0.7.17
-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_3.8.0 ]; then
- conda create --yes --name gatk_3.8.0 gatk=3.8
-fi
-if [ ! -d ${CONDA_ENVS}gatk_4.0.8.1 ]; then
- conda create --yes --name gatk_4.0.8.1 gatk4=4.0.8.1-0
-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
-if [ ! -d ${CONDA_ENVS}star_2.7.3a ]; then
- conda create --yes --name star_2.7.3a star=2.7.3a
-fi
-if [ ! -d ${CONDA_ENVS}liftover_357 ]; then
- conda create --yes --name liftover_357 ucsc-liftover==357
-fi
-if [ ! -d ${CONDA_ENVS}axtchain_377 ]; then
- conda create --yes --name axtchain_377 ucsc-axtchain==377
-fi
-if [ ! -d ${CONDA_ENVS}ribotish_0.2.4 ]; then
- conda create --name ribotish_0.2.4 ribotish=0.2.4
-fi
diff --git a/src/.conda_psmn.sh b/src/.conda_psmn.sh
deleted file mode 120000
index cbb3d9b5..00000000
--- a/src/.conda_psmn.sh
+++ /dev/null
@@ -1 +0,0 @@
-/Xnfs/lbmcdb/common/conda/init.sh
\ No newline at end of file
diff --git a/src/.update_config.sh b/src/.update_config.sh
deleted file mode 100644
index 2ea29fcf..00000000
--- a/src/.update_config.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-# update docker url
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container = "lbmc/|g' -i {}
-
-# update singularity url
-fd ".*config" -E "nf_modules" src/ -x perl -pe 's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g' -i {}
-
-# update singularity config
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg' -i {}
-
-# update in2p3 config
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n ccin2p3 {\n singularity.enabled = true\n singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg' -i {}
-fd ".*config" src/ -x perl -pe 's|container = "lbmc//sps/lbmc/common/singularity/(.*).img"|container = "lbmc/\1"|g' -i {}
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|singularity.cacheDir = "/sps/lbmc/common/singularity/"|singularity.cacheDir = "\$baseDir/.singularity_in2p3/"|mg' -i {}
-
-# we remove the ccin2p3_conda section
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe "s|\s*ccin2p3_conda {.*ccin2p3 {\n|\n ccin2p3 {\n|msg" -i {}
-
-# we update the psmn module to conda
-fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"\n\s*module = "(.*)/(.*)"|beforeScript = "source \$baseDir/.conda_psmn.sh"\n conda = "\$baseDir/.conda_envs/\L\1_\2"|mg' -i {}
-
-# we update the psmn queue to new cluster
-fd ".*config" src/ -x perl -0777pe 's|E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F|CLG6242deb384A,CLG6242deb384C,CLG5218deb192A,CLG5218deb192B,CLG5218deb192C,CLG5218deb192D,SLG5118deb96,SLG6142deb384A,SLG6142deb384B,SLG6142deb384C,SLG6142deb384D|mg' -i {}
-fd ".*config" src/ -x perl -0777pe 's|monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128|monointeldeb128|mg' -i {}
-fd ".*config" src/ -x perl -0777pe 's|openmp16|openmp32|mg' -i {}
-fd ".*config" src/ -x perl -0777pe 's|cpus = 16|cpus = 32|mg' -i {}
-fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
-
-# we update the psmn config to singularity
-fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n singularity.enabled = true\n singularity.cacheDir = "$baseDir/.singularity_psmn/"\n singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
-fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
-fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*scratch = true(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
-fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*stageInMode = "copy"\n\s*stageOutMode = "rsync"(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
diff --git a/src/.update_tools.sh b/src/.update_tools.sh
deleted file mode 100755
index 57af5db8..00000000
--- a/src/.update_tools.sh
+++ /dev/null
@@ -1,92 +0,0 @@
-#/bin/sh
-
-# A POSIX variable
-OPTIND=1
-
-# Initialize our own variables:
-tool=""
-version=""
-
-while getopts "h?v:t:p:" opt; do
- case "${opt}" in
- h|\?)
- echo "update_tools.sh -t toolname -v tool_version -p tool_previous_version"
- exit 0
- ;;
- v)
- version=${OPTARG}
- ;;
- p)
- prev_version=${OPTARG}
- ;;
- t)
- tool=${OPTARG}
- ;;
- esac
-done
-
-echo "tool=${tool}, version='${version}', previous version='${version}'"
-
-docker_tool_dir="src/docker_modules/"${tool}"/"
-echo ${docker_tool_dir}
-if [ -d ${docker_tool_dir} ]; then
- echo "docker module found for ${tool}."
- if [ -d ${docker_tool_dir}${version} ]; then
- echo "version already existing, skipping."
- else
- cp -R ${docker_tool_dir}${prev_version} ${docker_tool_dir}${version}
- sed -i "s|${prev_version}|${version}|g" "${docker_tool_dir}${version}/Dockerfile"
- sed -i "s|${prev_version}|${version}|g" "${docker_tool_dir}${version}/docker_init.sh"
- echo "docker_module for ${tool}:${version}, done."
- fi
-else
- echo "docker module not found for '${tool}', skipping."
-fi
-
-singularity_tool_dir="src/singularity_modules/"${tool}"/"
-echo ${singularity_tool_dir}
-if [ -d ${singularity_tool_dir} ]; then
- echo "singularity module found for $tool."
- if [ -d ${singularity_tool_dir}${version} ]; then
- echo "version already existing, skipping."
- else
- cp -R ${singularity_tool_dir}${prev_version} ${singularity_tool_dir}${version}
- sed -i "s|${prev_version}|${version}|g" "${singularity_tool_dir}${version}/${tool}.def"
- sed -i "s|${prev_version}|${version}|g" "${singularity_tool_dir}${version}/build.sh"
- echo "singularity_module for ${tool}:${version}, done."
- fi
-else
- echo "singularity module not found for '${tool}', skipping."
-fi
-
-nf_tool_dir="src/nf_modules/"$tool"/"
-echo $nf_tool_dir
-if [ -d ${nf_tool_dir} ]; then
- echo "nf module found for ${tool}."
- find ${nf_tool_dir} -maxdepth 1 -mindepth 1 -type f -name "*.config" |
- awk "{system(\"sed -i \\\"s|${prev_version}|${version}|g\\\" \"\$0)}"
- echo "nf_module for ${tool}:${version}, done."
-else
- echo "nf module not found for '${tool}', skipping."
-fi
-
-psmn_modules_dir="src/psmn_modules/.git/"
-if [ ! -d ${nf_tool_dir} ]; then
- git submodule init && \
- git submodule update
-fi
-psmn_tool_app_dir="src/psmn_modules/apps/"${tool}"/"
-psmn_tool_module_dir="src/psmn_modules/modulefiles/"${tool}"/"
-echo ${psmn_tool_app_dir}
-if [ -d ${psmn_tool_app_dir} ]; then
- echo "psmn module found for ${tool}."
- cp ${psmn_tool_app_dir}/install_${prev_version}.sh \
- ${psmn_tool_app_dir}/install_${version}.sh
- sed -i "s|$prev_version|$version|g" ${psmn_tool_app_dir}/install_${version}.sh
- cp ${psmn_tool_module_dir}/${prev_version}.lua \
- ${psmn_tool_module_dir}/${version}.lua
- sed -i "s|${prev_version}|${version}|g" ${psmn_tool_module_dir}/${version}.lua
- echo "psmn_module for ${tool}:${version}, done."
-else
- echo "psmn module not found for '${tool}', skipping."
-fi
--
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