Merge branch 'submission' into 'main'

fasterq hidden macs2 picard

See merge request !13

.gitlab-ci.yml

@@ -36,7 +36,36 @@ image:
 
 ## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST
 
-
+hiddendomains-31-test:
+  extends: .templateTest
+  variables:
+    BASENAME: hiddendomains
+    TAG: 31
+    RECIPE_PATH: recipes/peakcallers/hiddendomains
+
+macs2-2271-test:
+  extends: .templateTest
+  variables:
+    BASENAME: macs2
+    TAG: 2271
+    RECIPE_PATH: recipes/peakcallers/macs2
+
+
+picardtools-2221-test:
+  extends: .templateTest
+  variables:
+    BASENAME: picardtools
+    TAG: 2221
+    RECIPE_PATH: recipes/analysis-suites/picardtools
+
+picardtools-2271-test:
+  extends: .templateTest
+  variables:
+    BASENAME: picardtools
+    TAG: 2271
+    RECIPE_PATH: recipes/analysis-suites/picardtools
+
+    
 #####################
 # Image analysis
 #####################

recipes/analysis-suites/picardtools/Singularity.picardtools-2221

+BootStrap: docker
+From: ubuntu:bionic
+
+%help
+
+	This singularity installs picard tools v 2.22.1
+
+%post
+    # ~~~~~~ General setup and folder creation ~~~~~~ #
+    
+    apt-get update && apt-get install -y wget libreadline-dev
+        
+    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
+	
+    # ~~~~~ MINICONDA ~~~~~ #
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /conda && \
+    rm -f Miniconda3-latest-Linux-x86_64.sh
+    export PATH="/conda/bin:${PATH}"
+    
+    # ~~~~ R v 4.1.2 ~~~~~~ #
+    conda install -c conda-forge r-base=4.1.2
+    
+    # ~~~~~ PICARD TOOLS ~~~~~ #
+	conda install -y -c bioconda picard=2.22.1
+	
+	
+%environment
+    export PATH="${PATH}:/conda/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
+

recipes/analysis-suites/picardtools/Singularity.picardtools-2271

+BootStrap: docker
+From: ubuntu:bionic
+
+%help
+
+	This singularity installs picard tools v 2.27.1
+
+%post
+    # ~~~~~~ General setup and folder creation ~~~~~~ #
+    
+    apt-get update && apt-get install -y wget libreadline-dev
+        
+    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
+	
+    # ~~~~~ MINICONDA ~~~~~ #
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
+    bash Miniconda3-latest-Linux-x86_64.sh -b -p /conda && \
+    rm -f Miniconda3-latest-Linux-x86_64.sh
+    export PATH="/conda/bin:${PATH}"
+    
+    # ~~~~ R v 4.1.2 ~~~~~~ #
+    conda install -c conda-forge r-base=4.1.2
+    
+    # ~~~~~ PICARD TOOLS ~~~~~ #
+	conda install -y -c bioconda picard=2.27.1
+	
+	
+%environment
+    export PATH="${PATH}:/conda/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
+

recipes/peakcallers/hiddendomains/Singularity.hiddendomains-31

+BootStrap: docker
+From: ubuntu:xenial
+
+%help
+    This singularity install hiddenDomains v3.1
+
+%post
+
+    # ~~~~~~ General setup and folder creation ~~~~~~ #
+    
+    apt-get update && apt-get install -y wget bzip2
+    
+    export LC_ALL=en_US.UTF-8
+    export LC_COLLATE=C
+    export LC_CTYPE=C
+    export LC_MEASUREMENT=C
+    export LC_MESSAGES=C
+    export LC_MONETARY=C
+    export LC_PAPER=C
+    export LC_TIME=C
+    export LANG=C.UTF-8
+    
+    # ~~~~~ MINICONDA 3.4.0.5 ~~~~~ #
+    wget https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh && \
+    bash Miniconda3-4.6.14-Linux-x86_64.sh -b -p /conda && \
+    rm -f Miniconda3-4.6.14-Linux-x86_64.sh
+    export PATH="/conda/bin:${PATH}"
+    
+    # ~~~~~ perl 5.32.1 ~~~~~~~#
+    conda install -c conda-forge perl=5.32.1
+    
+    # ~~~~ R v 4.1.2 ~~~~~~ #
+    conda install -c conda-forge r-base=4.1.2
+    
+    # ~~~ r-depmixs4 v1.5_0 ~~~~#
+    conda install -c conda-forge r-depmixs4=1.5_0
+    
+    #~~~~ r-hiddenmarkov v1.8_13 ~~~#
+    conda install -c conda-forge r-hiddenmarkov=1.8_13
+    
+    # ~~~~~ hiddendomains v3.1 ~~~~~ #
+    conda install -y -c bioconda hiddendomains=3.1
+    
+%environment
+    export PATH="${PATH}:/conda/bin"
+    export LC_ALL=en_US.UTF-8
+    export LC_COLLATE=C
+    export LC_CTYPE=C
+    export LC_MEASUREMENT=C
+    export LC_MESSAGES=C
+    export LC_MONETARY=C
+    export LC_PAPER=C
+    export LC_TIME=C
+    export LANG=C.UTF-8
+    
+
+%labels
+    Author Nicolas Descostes
+    Version v0.0.5
+

recipes/peakcallers/macs2/Singularity.macs2-2271

+Bootstrap: docker
+From: dceoy/macs2:latest
+
+%runscript
+    echo "Running container dceoy/macs2, macs2 v2.2.7.1"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects