gapseq
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[feature request] conda package
The installation for gapseq requires root access to the machine which is often not the case for servers. It would be awesome if there was a conda package to facilitate a more accessible installation.
Hi @cdiener thanks for pointing this out! We hope to have a conda package available soon! Right now, I added some hints to the readme how to install all needed dependencies from conda without root rights.
Awesome thanks! A working docker or singularity image would also be an alternative if that is easier.
good idea thanks! we try to come up with some alternative installation in the near future :)
just as intermediate solution, we added a conda installation tutorial
Sure, no hurry. We packaged it as a docker image for our workflows for now: https://github.com/Gibbons-Lab/gapseq-docker. Though I noticed there are some dependencies that are not mentioned, like curl for instance.
@jotech any updates on creating the bioconda recipe? As illustrated with your conda installation tutorial, a conda recipe really helps developers (eg., of bioinformatics pipelines) install & maintain the dependencies of all software.
In regards to the conda install tutorial, a bit simpler approach:
conda env yaml file:
channels:
- conda-forge
- bioconda
dependencies:
- bash
- r
- perl
- parallel
- gawk
- sed
- grep
- bc
- git
- coreutils
- wget
- barrnap
- bedtools
- exonerate
- glpk
- hmmer
- blast
- bioconda::libsbml
- r-data.table
- r-stringr
- r-stringi
- r-getopt
- r-doParallel
- r-foreach
- r-r.utils
- r-sybil
- r-biocmanager
- bioconductor-biostrings
- r-jsonlite
- r-renv
Create conda env:
mamba env create -n gapseq -f gapseq_env.yaml
Additional R package install:
R -e 'renv::install(c("glpkAPI", "CHNOSZ"))'
In regards to the gapseq install instructions, I'm guessing that you meant:
bash ./src/update_sequences.sh
instead of:
src/./update_sequences.sh
Thanks @nick-youngblut. I agree that a conda env yaml file would clean up the instructions. I'll update the conda instructions in January.
Once this is available as a conda installation I'm going to add it as a module in my https://github.com/jolespin/veba pipeline. The publication just got accepted and should be out soon.