From bda5e76552def9df4eff481104e8904e4256e26a Mon Sep 17 00:00:00 2001
From: Nicolas Descostes <nicolas.descostes@embl.it>
Date: Tue, 10 Oct 2023 13:33:46 +0200
Subject: [PATCH] spikchipcustom 102
---
.gitlab-ci.yml | 7 +++
.../Singularity.spikchipcustom-v102 | 48 +++++++++++++++++++
2 files changed, 55 insertions(+)
create mode 100644 recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v102
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6545057..e325734 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -35,6 +35,13 @@ image:
#####################
## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST
+spikchipcustom-v102-test:
+ extends: .templateTest
+ variables:
+ BASENAME: spikchipcustom
+ TAG: v102
+ RECIPE_PATH: recipes/chipseq/spikchipcustom
+
#####################
## Include
diff --git a/recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v102 b/recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v102
new file mode 100644
index 0000000..b7a4967
--- /dev/null
+++ b/recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v102
@@ -0,0 +1,48 @@
+BootStrap: docker
+From: ubuntu
+
+
+%help
+
+ This singularity installs spikchip. See repository https://github.com/eblancoga/spikChIP
+
+%post
+ # ~~~~~~ General setup and folder creation ~~~~~~ #
+
+ apt update && DEBIAN_FRONTEND=noninteractive apt install -y gcc git libz-dev make r-base curl samtools software-properties-common gawk bash
+
+ export LC_ALL=C
+ export LC_CTYPE=C
+ export LC_COLLATE=C
+ export LC_TIME=C
+ export LC_MESSAGES=C
+ export LC_MONETARY=C
+ export LC_PAPER=C
+ export LC_MEASUREMENT=C
+
+ # ~~~~~ seqcode ~~~~~ #
+ curl -L https://github.com/eblancoga/seqcode/archive/master.tar.gz -o seqcode.tar.gz && tar -xvzf seqcode.tar.gz && rm seqcode.tar.gz && cd seqcode-main/ && make all && cd ..
+
+ # ~~~~~ samtools ~~~~~ #
+ add-apt-repository universe && apt update && apt install -y samtools
+
+ # ~~~~~ affy and MASS ~~~~~ #
+ R --slave -e 'install.packages(c("BiocManager", "MASS"), repos="https://cloud.r-project.org/")' && R --slave -e 'BiocManager::install(c("affy"))'
+
+ # ~~~~~ spikchip ~~~~~ #
+ curl -L https://github.com/descostesn/spikChIP/archive/refs/tags/1.0.2.tar.gz -o spikchip.tar.gz && tar -xvzf spikchip.tar.gz && rm spikchip.tar.gz && cd spikChIP-1.0.2/ && rm -r examples && cd ..
+
+%environment
+ export PATH="${PATH}:/spikChIP-1.0.2:/seqcode-main/bin"
+ export LC_ALL=C
+ export LC_CTYPE=C
+ export LC_COLLATE=C
+ export LC_TIME=C
+ export LC_MESSAGES=C
+ export LC_MONETARY=C
+ export LC_PAPER=C
+ export LC_MEASUREMENT=C
+
+%labels
+ Author Nicolas Descostes
+ Version v0.0.1
--
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