diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 6545057d4cfb94bca740d860d38f49edc713b30a..e3257341aff161eec9984f0a2f00d382f5c4b4a6 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 0000000000000000000000000000000000000000..b7a49670181112b2434b62f9ece979b41cabe54e --- /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