diff --git a/recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v100 b/recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v100 new file mode 100644 index 0000000000000000000000000000000000000000..e0924ecd05897077d9de83aab34323cfa420fd21 --- /dev/null +++ b/recipes/chipseq/spikchipcustom/Singularity.spikchipcustom-v100 @@ -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/1.0.0.tar.gz -o spikchip.tar.gz && tar -xvzf spikchip.tar.gz && rm spikchip.tar.gz && cd spikChIP-1.0.0/ && rm -r examples && cd .. + +%environment + export PATH="${PATH}:/spikChIP-1.0.0:/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 v0.0.2