Commit cfdaca57 authored by Blaise Li's avatar Blaise Li
Browse files

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

parents 94a9a806 b1c06d55
libhts @ 1e3695f8
Subproject commit 2afd8597877c51add81affc53f930d23e875a9e1
Subproject commit 1e3695f8dc0f62b976f0a1b3da88a0fd1347f83a
all: run_pipeline
# Should depend on the rest of the repository.
run_pipeline: run_pipeline.def
sudo singularity build run_pipeline run_pipeline.def
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.
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