From 3946437084adccd91bb3293473be0101703ea7fb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 13 Apr 2021 15:20:09 +0200
Subject: [PATCH] change path for the shared singularity img at the ccin2p3

---
 src/.singularity_in2p3                            | 1 +
 src/.singularity_in2p3/lbmc-bcftools-1.7.img      | 1 -
 src/.singularity_in2p3/lbmc-bedtools-2.25.0.img   | 1 -
 src/.singularity_in2p3/lbmc-bioawk-1.0.img        | 1 -
 src/.singularity_in2p3/lbmc-bowtie-1.2.2.img      | 1 -
 src/.singularity_in2p3/lbmc-bowtie2-2.3.4.1.img   | 1 -
 src/.singularity_in2p3/lbmc-bwa-0.7.17.img        | 1 -
 src/.singularity_in2p3/lbmc-canu-1.6.img          | 1 -
 src/.singularity_in2p3/lbmc-cutadapt-1.14.img     | 1 -
 src/.singularity_in2p3/lbmc-cutadapt-1.15.img     | 1 -
 src/.singularity_in2p3/lbmc-cutadapt-2.1.img      | 1 -
 src/.singularity_in2p3/lbmc-deeptools-3.0.2.img   | 1 -
 src/.singularity_in2p3/lbmc-deeptools-3.1.1.img   | 1 -
 src/.singularity_in2p3/lbmc-fastp-0.19.7.img      | 1 -
 src/.singularity_in2p3/lbmc-fastqc-0.11.5.img     | 1 -
 src/.singularity_in2p3/lbmc-file_handle-0.1.1.img | 1 -
 src/.singularity_in2p3/lbmc-gatk-4.0.8.1.img      | 1 -
 src/.singularity_in2p3/lbmc-hisat2-2.0.0.img      | 1 -
 src/.singularity_in2p3/lbmc-hisat2-2.1.0.img      | 1 -
 src/.singularity_in2p3/lbmc-htseq-0.11.2.img      | 1 -
 src/.singularity_in2p3/lbmc-htseq-0.8.0.img       | 1 -
 src/.singularity_in2p3/lbmc-kallisto-0.43.1.img   | 1 -
 src/.singularity_in2p3/lbmc-kallisto-0.44.0.img   | 1 -
 src/.singularity_in2p3/lbmc-macs2-2.1.2.img       | 1 -
 src/.singularity_in2p3/lbmc-multiqc-1.0.img       | 1 -
 src/.singularity_in2p3/lbmc-multiqc-1.7.img       | 1 -
 src/.singularity_in2p3/lbmc-music-6613c53.img     | 1 -
 src/.singularity_in2p3/lbmc-picard-2.18.11.img    | 1 -
 src/.singularity_in2p3/lbmc-pigz-2.4.img          | 1 -
 src/.singularity_in2p3/lbmc-r-3.5.3.img           | 1 -
 src/.singularity_in2p3/lbmc-rsem-1.3.0.img        | 1 -
 src/.singularity_in2p3/lbmc-salmon-0.8.2.img      | 1 -
 src/.singularity_in2p3/lbmc-sambamba-0.6.7.img    | 1 -
 src/.singularity_in2p3/lbmc-samblaster-0.1.24.img | 1 -
 src/.singularity_in2p3/lbmc-samtools-1.7.img      | 1 -
 src/.singularity_in2p3/lbmc-sratoolkit-2.8.2.img  | 1 -
 src/.singularity_in2p3/lbmc-star-2.7.3a.img       | 1 -
 src/.singularity_in2p3/lbmc-subread-1.6.4.img     | 1 -
 src/.singularity_in2p3/lbmc-tophat-2.1.1.img      | 1 -
 src/.singularity_in2p3/lbmc-trimmomatic-0.36.img  | 1 -
 src/.singularity_in2p3/lbmc-ucsc-375.img          | 1 -
 src/.singularity_in2p3/lbmc-umi_tools-1.0.0.img   | 1 -
 src/.singularity_in2p3/lbmc-urqt-d62c1f8.img      | 1 -
 43 files changed, 1 insertion(+), 42 deletions(-)
 create mode 120000 src/.singularity_in2p3
 delete mode 120000 src/.singularity_in2p3/lbmc-bcftools-1.7.img
 delete mode 120000 src/.singularity_in2p3/lbmc-bedtools-2.25.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-bioawk-1.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-bowtie-1.2.2.img
 delete mode 120000 src/.singularity_in2p3/lbmc-bowtie2-2.3.4.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-bwa-0.7.17.img
 delete mode 120000 src/.singularity_in2p3/lbmc-canu-1.6.img
 delete mode 120000 src/.singularity_in2p3/lbmc-cutadapt-1.14.img
 delete mode 120000 src/.singularity_in2p3/lbmc-cutadapt-1.15.img
 delete mode 120000 src/.singularity_in2p3/lbmc-cutadapt-2.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-deeptools-3.0.2.img
 delete mode 120000 src/.singularity_in2p3/lbmc-deeptools-3.1.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-fastp-0.19.7.img
 delete mode 120000 src/.singularity_in2p3/lbmc-fastqc-0.11.5.img
 delete mode 120000 src/.singularity_in2p3/lbmc-file_handle-0.1.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-gatk-4.0.8.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-hisat2-2.0.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-hisat2-2.1.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-htseq-0.11.2.img
 delete mode 120000 src/.singularity_in2p3/lbmc-htseq-0.8.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-kallisto-0.43.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-kallisto-0.44.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-macs2-2.1.2.img
 delete mode 120000 src/.singularity_in2p3/lbmc-multiqc-1.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-multiqc-1.7.img
 delete mode 120000 src/.singularity_in2p3/lbmc-music-6613c53.img
 delete mode 120000 src/.singularity_in2p3/lbmc-picard-2.18.11.img
 delete mode 120000 src/.singularity_in2p3/lbmc-pigz-2.4.img
 delete mode 120000 src/.singularity_in2p3/lbmc-r-3.5.3.img
 delete mode 120000 src/.singularity_in2p3/lbmc-rsem-1.3.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-salmon-0.8.2.img
 delete mode 120000 src/.singularity_in2p3/lbmc-sambamba-0.6.7.img
 delete mode 120000 src/.singularity_in2p3/lbmc-samblaster-0.1.24.img
 delete mode 120000 src/.singularity_in2p3/lbmc-samtools-1.7.img
 delete mode 120000 src/.singularity_in2p3/lbmc-sratoolkit-2.8.2.img
 delete mode 120000 src/.singularity_in2p3/lbmc-star-2.7.3a.img
 delete mode 120000 src/.singularity_in2p3/lbmc-subread-1.6.4.img
 delete mode 120000 src/.singularity_in2p3/lbmc-tophat-2.1.1.img
 delete mode 120000 src/.singularity_in2p3/lbmc-trimmomatic-0.36.img
 delete mode 120000 src/.singularity_in2p3/lbmc-ucsc-375.img
 delete mode 120000 src/.singularity_in2p3/lbmc-umi_tools-1.0.0.img
 delete mode 120000 src/.singularity_in2p3/lbmc-urqt-d62c1f8.img

diff --git a/src/.singularity_in2p3 b/src/.singularity_in2p3
new file mode 120000
index 00000000..7f86c054
--- /dev/null
+++ b/src/.singularity_in2p3
@@ -0,0 +1 @@
+/sps/lbmc/common/singularity/
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-bcftools-1.7.img b/src/.singularity_in2p3/lbmc-bcftools-1.7.img
deleted file mode 120000
index 3f3b72a6..00000000
--- a/src/.singularity_in2p3/lbmc-bcftools-1.7.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-bcftools-1.7.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-bedtools-2.25.0.img b/src/.singularity_in2p3/lbmc-bedtools-2.25.0.img
deleted file mode 120000
index 2003d114..00000000
--- a/src/.singularity_in2p3/lbmc-bedtools-2.25.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-bedtools-2.25.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-bioawk-1.0.img b/src/.singularity_in2p3/lbmc-bioawk-1.0.img
deleted file mode 120000
index 56d68b28..00000000
--- a/src/.singularity_in2p3/lbmc-bioawk-1.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-bioawk-1.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-bowtie-1.2.2.img b/src/.singularity_in2p3/lbmc-bowtie-1.2.2.img
deleted file mode 120000
index 0977cfa4..00000000
--- a/src/.singularity_in2p3/lbmc-bowtie-1.2.2.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-bowtie-1.2.2.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-bowtie2-2.3.4.1.img b/src/.singularity_in2p3/lbmc-bowtie2-2.3.4.1.img
deleted file mode 120000
index da3b13a0..00000000
--- a/src/.singularity_in2p3/lbmc-bowtie2-2.3.4.1.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-bowtie2-2.3.4.1.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-bwa-0.7.17.img b/src/.singularity_in2p3/lbmc-bwa-0.7.17.img
deleted file mode 120000
index d6c0b9d7..00000000
--- a/src/.singularity_in2p3/lbmc-bwa-0.7.17.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-bwa-0.7.17.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-canu-1.6.img b/src/.singularity_in2p3/lbmc-canu-1.6.img
deleted file mode 120000
index 202c4a12..00000000
--- a/src/.singularity_in2p3/lbmc-canu-1.6.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-canu-1.6.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-cutadapt-1.14.img b/src/.singularity_in2p3/lbmc-cutadapt-1.14.img
deleted file mode 120000
index 5a40d3d0..00000000
--- a/src/.singularity_in2p3/lbmc-cutadapt-1.14.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-cutadapt-1.14.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-cutadapt-1.15.img b/src/.singularity_in2p3/lbmc-cutadapt-1.15.img
deleted file mode 120000
index b7fe3699..00000000
--- a/src/.singularity_in2p3/lbmc-cutadapt-1.15.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-cutadapt-1.15.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-cutadapt-2.1.img b/src/.singularity_in2p3/lbmc-cutadapt-2.1.img
deleted file mode 120000
index bfe89443..00000000
--- a/src/.singularity_in2p3/lbmc-cutadapt-2.1.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-cutadapt-2.1.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-deeptools-3.0.2.img b/src/.singularity_in2p3/lbmc-deeptools-3.0.2.img
deleted file mode 120000
index 20fac04f..00000000
--- a/src/.singularity_in2p3/lbmc-deeptools-3.0.2.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-deeptools-3.0.2.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-deeptools-3.1.1.img b/src/.singularity_in2p3/lbmc-deeptools-3.1.1.img
deleted file mode 120000
index cd9b1e8d..00000000
--- a/src/.singularity_in2p3/lbmc-deeptools-3.1.1.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-deeptools-3.1.1.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-fastp-0.19.7.img b/src/.singularity_in2p3/lbmc-fastp-0.19.7.img
deleted file mode 120000
index aec2258a..00000000
--- a/src/.singularity_in2p3/lbmc-fastp-0.19.7.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-fastp-0.19.7.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-fastqc-0.11.5.img b/src/.singularity_in2p3/lbmc-fastqc-0.11.5.img
deleted file mode 120000
index 939ac3cf..00000000
--- a/src/.singularity_in2p3/lbmc-fastqc-0.11.5.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-fastqc-0.11.5.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-file_handle-0.1.1.img b/src/.singularity_in2p3/lbmc-file_handle-0.1.1.img
deleted file mode 120000
index 50396d25..00000000
--- a/src/.singularity_in2p3/lbmc-file_handle-0.1.1.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-file_handle-0.1.1.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-gatk-4.0.8.1.img b/src/.singularity_in2p3/lbmc-gatk-4.0.8.1.img
deleted file mode 120000
index f398e91f..00000000
--- a/src/.singularity_in2p3/lbmc-gatk-4.0.8.1.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-gatk-4.0.8.1.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-hisat2-2.0.0.img b/src/.singularity_in2p3/lbmc-hisat2-2.0.0.img
deleted file mode 120000
index 24c7eb73..00000000
--- a/src/.singularity_in2p3/lbmc-hisat2-2.0.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-hisat2-2.0.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-hisat2-2.1.0.img b/src/.singularity_in2p3/lbmc-hisat2-2.1.0.img
deleted file mode 120000
index b210e78b..00000000
--- a/src/.singularity_in2p3/lbmc-hisat2-2.1.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-hisat2-2.1.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-htseq-0.11.2.img b/src/.singularity_in2p3/lbmc-htseq-0.11.2.img
deleted file mode 120000
index c2e222e8..00000000
--- a/src/.singularity_in2p3/lbmc-htseq-0.11.2.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-htseq-0.11.2.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-htseq-0.8.0.img b/src/.singularity_in2p3/lbmc-htseq-0.8.0.img
deleted file mode 120000
index d9761928..00000000
--- a/src/.singularity_in2p3/lbmc-htseq-0.8.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-htseq-0.8.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-kallisto-0.43.1.img b/src/.singularity_in2p3/lbmc-kallisto-0.43.1.img
deleted file mode 120000
index f0bc3cb4..00000000
--- a/src/.singularity_in2p3/lbmc-kallisto-0.43.1.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-kallisto-0.43.1.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-kallisto-0.44.0.img b/src/.singularity_in2p3/lbmc-kallisto-0.44.0.img
deleted file mode 120000
index f5a1df90..00000000
--- a/src/.singularity_in2p3/lbmc-kallisto-0.44.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-kallisto-0.44.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-macs2-2.1.2.img b/src/.singularity_in2p3/lbmc-macs2-2.1.2.img
deleted file mode 120000
index 3507efe4..00000000
--- a/src/.singularity_in2p3/lbmc-macs2-2.1.2.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-macs2-2.1.2.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-multiqc-1.0.img b/src/.singularity_in2p3/lbmc-multiqc-1.0.img
deleted file mode 120000
index 2c95d54b..00000000
--- a/src/.singularity_in2p3/lbmc-multiqc-1.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-multiqc-1.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-multiqc-1.7.img b/src/.singularity_in2p3/lbmc-multiqc-1.7.img
deleted file mode 120000
index df7f68b5..00000000
--- a/src/.singularity_in2p3/lbmc-multiqc-1.7.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-multiqc-1.7.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-music-6613c53.img b/src/.singularity_in2p3/lbmc-music-6613c53.img
deleted file mode 120000
index a0f66ea1..00000000
--- a/src/.singularity_in2p3/lbmc-music-6613c53.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-music-6613c53.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-picard-2.18.11.img b/src/.singularity_in2p3/lbmc-picard-2.18.11.img
deleted file mode 120000
index d2373a62..00000000
--- a/src/.singularity_in2p3/lbmc-picard-2.18.11.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-picard-2.18.11.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-pigz-2.4.img b/src/.singularity_in2p3/lbmc-pigz-2.4.img
deleted file mode 120000
index 25f59290..00000000
--- a/src/.singularity_in2p3/lbmc-pigz-2.4.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-pigz-2.4.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-r-3.5.3.img b/src/.singularity_in2p3/lbmc-r-3.5.3.img
deleted file mode 120000
index 447fc146..00000000
--- a/src/.singularity_in2p3/lbmc-r-3.5.3.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-r-3.5.3.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-rsem-1.3.0.img b/src/.singularity_in2p3/lbmc-rsem-1.3.0.img
deleted file mode 120000
index 8230e003..00000000
--- a/src/.singularity_in2p3/lbmc-rsem-1.3.0.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-rsem-1.3.0.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-salmon-0.8.2.img b/src/.singularity_in2p3/lbmc-salmon-0.8.2.img
deleted file mode 120000
index ebe41773..00000000
--- a/src/.singularity_in2p3/lbmc-salmon-0.8.2.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-salmon-0.8.2.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-sambamba-0.6.7.img b/src/.singularity_in2p3/lbmc-sambamba-0.6.7.img
deleted file mode 120000
index e001f82d..00000000
--- a/src/.singularity_in2p3/lbmc-sambamba-0.6.7.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-sambamba-0.6.7.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-samblaster-0.1.24.img b/src/.singularity_in2p3/lbmc-samblaster-0.1.24.img
deleted file mode 120000
index 242ae80e..00000000
--- a/src/.singularity_in2p3/lbmc-samblaster-0.1.24.img
+++ /dev/null
@@ -1 +0,0 @@
-/sps/lbmc/common/singularity/lbmc-samblaster-0.1.24.img
\ No newline at end of file
diff --git a/src/.singularity_in2p3/lbmc-samtools-1.7.img b/src/.singularity_in2p3/lbmc-samtools-1.7.img
deleted file mode 120000
index 8f513f76..00000000
--- a/src/.singularity_in2p3/lbmc-samtools-1.7.img
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