[feature request] conda package

[cdiener]

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.

[jotech]

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.

[cdiener]

Awesome thanks! A working docker or singularity image would also be an alternative if that is easier.

[jotech]

good idea thanks! we try to come up with some alternative installation in the near future :)

[jotech]

just as intermediate solution, we added a conda installation tutorial

[cdiener]

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.

[nick-youngblut]

@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.

[nick-youngblut]

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

[Waschina]

Thanks @nick-youngblut. I agree that a conda env yaml file would clean up the instructions. I'll update the conda instructions in January.

[jolespin]

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.

[cmkobel]

@jotech in order for a bioconda package to be effective you should make frequent releases (maybe, at least once a year). The current release (https://github.com/jotech/gapseq/releases/tag/v1.2) is more than two years old even though you had commits a few weeks ago (https://github.com/jotech/gapseq/commit/2d739a56a26a1eb9841b0b4999b3498452923406). Are there any plans to make a new release of gapseq that includes the changes to the development version?