From d8d6d217387c4128b2d3c4fbf095fdc4ac5eaf15 Mon Sep 17 00:00:00 2001
From: Nicolas Descostes <nicolas.descostes@embl.it>
Date: Sat, 16 Apr 2022 08:37:05 +0000
Subject: [PATCH] bowtie2
---
.gitlab-ci.yml | 2 +-
recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 | 12 ++++++++++++
recipes/mapping/bowtie2/Singularity.bowtie2-245 | 12 ++++++++++++
yaml-files/quality-control/fastqc-test.backup | 6 +++---
4 files changed, 28 insertions(+), 4 deletions(-)
create mode 100644 recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
create mode 100644 recipes/mapping/bowtie2/Singularity.bowtie2-245
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 88585d2..85fc2f5 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -44,7 +44,7 @@ include:
- local: "yaml-files/image-analysis/deeplabcut-deploy.yaml"
#####################
-## Quality control
+# Mapping
#####################
include:
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
new file mode 100644
index 0000000..71bebf4
--- /dev/null
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
@@ -0,0 +1,12 @@
+Bootstrap: docker
+From: biocontainers/bowtie2:v2.4.1_cv1
+
+%runscript
+ echo "Running container biocontainers/bowtie2:v2.4.1_cv1, Bowtie v2.4.1"
+ exec /bin/bash "$@"
+
+%post
+ mkdir /cluster /work /tsd /projects
+
+%labels
+ Author Nicolas Descostes
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-245 b/recipes/mapping/bowtie2/Singularity.bowtie2-245
new file mode 100644
index 0000000..8b9822a
--- /dev/null
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-245
@@ -0,0 +1,12 @@
+Bootstrap: docker
+From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
+
+%runscript
+ echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
+ exec /bin/bash "$@"
+
+%post
+ mkdir /cluster /work /tsd /projects
+
+%labels
+ Author Nicolas Descostes
diff --git a/yaml-files/quality-control/fastqc-test.backup b/yaml-files/quality-control/fastqc-test.backup
index e7ad88c..a287f61 100644
--- a/yaml-files/quality-control/fastqc-test.backup
+++ b/yaml-files/quality-control/fastqc-test.backup
@@ -3,7 +3,7 @@ fastqc-0119cv7-test:
variables:
BASENAME: fastqc
TAG: 0119cv7
- RECIPE_PATH: recipes/quality-control/fastqc/
+ RECIPE_PATH: recipes/quality-control/fastqc
fastqc-0119cv8-test:
@@ -11,11 +11,11 @@ fastqc-0119cv8-test:
variables:
BASENAME: fastqc
TAG: 0119cv8
- RECIPE_PATH: recipes/quality-control/fastqc/
+ RECIPE_PATH: recipes/quality-control/fastqc
fastqc-0119cv6-test:
extends: .templateTest
variables:
BASENAME: fastqc
TAG: 0119cv6
- RECIPE_PATH: recipes/quality-control/fastqc/
+ RECIPE_PATH: recipes/quality-control/fastqc
--
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