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LieberInstitute / SPEAQeasy

SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.
http://lieberinstitute.github.io/SPEAQeasy
MIT License
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Sharing pipeline is not as trivial as suggested #57

Closed Nick-Eagles closed 3 years ago

Nick-Eagles commented 4 years ago

In the README and manuscript, we claim that one can copy a main script (e.g. run_pipeline_sge.sh), modify the path to nextflow in the copied script, and now SPEAQeasy can be shared by another user in a different directory. There is one obstacle to this currently:

bam2wig.py from RSeQC relies on other dependencies installed with python3 -m pip install --user RSeQC==3.0.1, but these cannot be installed globally with root privileges. This problem does not affect docker users.

andrewejaffe commented 4 years ago

We should just make the coverage step optional, where the default is to not run it.

On Fri, Jul 17, 2020, 12:07 PM Nick-Eagles notifications@github.com wrote:

In the README and manuscript, we claim that one can copy a main script (e.g. run_pipeline_sge.sh), modify the path to nextflow in the copied script, and now SPEAQeasy can be shared by another user in a different directory. There is one obstacle to this currently:

bam2wig.py from RSeQC relies on other dependencies installed with python3 -m pip install --user RSeQC==3.0.1, but these cannot be installed globally with root privileges. This problem does not affect docker users.

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Nick-Eagles commented 4 years ago

So just the counts and variant calling are always run? Just making sure, since we already have the "full coverage" step as optional, but not this coverage step leading to the "expressed regions" step.

lcolladotor commented 4 years ago

In our meeting today we decided to make the ER quantification step optional, following what Andrew had suggested earlier. Although that only delays the bam2wig.py issue for users who want to use it. So it might be useful to leave a note about this on the docs.

Nick-Eagles commented 3 years ago

I'm closing this issue, as the additional pip command required for the coverage steps is now documented here