Merge branch 'submission' into 'main'

spikchipcustom 102

See merge request !37

.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

recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v102

+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