Merge branch 'master' of gitlab.pasteur.fr:bli/bioinfo_utils

libhts @ 1e3695f8

-Subproject commit 2afd8597877c51add81affc53f930d23e875a9e1
+Subproject commit 1e3695f8dc0f62b976f0a1b3da88a0fd1347f83a

singularity/Makefile

+all: run_pipeline
+
+# Should depend on the rest of the repository.
+run_pipeline: run_pipeline.def
+	sudo singularity build run_pipeline run_pipeline.def

singularity/README_singularity.md

+Running the pipelines using singularity
+=======================================
+
+This folder contains a recipe to build a singularity container for the
+workflows and their dependencies.
+
+To build the container run the following command:
+
+    sudo singularity build run_pipeline run_pipeline.def
+
+
+Of course, you need singularity, and administrative rights to do that (that's
+part of how singularity works).
+
+This folder also contain a shell script wrapper and aliases that will run one
+of the workflows using the container. The built container should be present in
+the same directory as the wrapper and aliases.
+
+Each alias will run a specific pipeline, depending on its name.
+There may be several aliases for a same pipeline.
+Here are the aliases available for each pipeline: 
+
+* sRNA-seq
+    - `run_sRNA-seq_pipeline`
+    - `run_small_RNA-seq_pipeline`
+* GRO-seq
+    - `run_GRO-seq_pipeline`
+    - `run_PRO-seq_pipeline`
+* RNA-seq
+    - `run_RNA-seq_pipeline`
+* Degradme-seq
+    - `run_Degradome-seq_pipeline`
+* Ribo-seq
+    - `run_Ribo-seq_pipeline`
+* iCLIP (which has a special "non-seq" name)
+    - `run_iCLIP-seq_pipeline`
+    - `run_iCLIP_pipeline`
+
+### TODO
+
+The container takes a long time to build. Maybe it should be split into smaller
+bits, used by a larger one.