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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
72 stars 40 forks source link

missing depencies in the documentation #416

Closed oliviermattelaer closed 4 years ago

oliviermattelaer commented 4 years ago

Our HPC guidelines strongly discourages us to use conda for the installation (and since I'm one of the sys-admin I have to obey the rule strictly). Therefore I'm doing a manual installation of all the dependencies (via easybuild) first and then cloning the code from github.

However when trying to import the python module, ipyrad fails to load because

  1. MUSCLE is not installed (this is not indicated in your dependencies
  2. SAMtools is not installed
  3. bedtools is not installed
  4. BWA
  5. VSEARCH Should not you update the documentation?

I have also notice that you seem to have dependencies to jedi/jupyter (but those might be implicit due to some of the other dependencies).

I will update the list if I found more hidden dependencies.

Cheers,

Olivier

PS: Do you have a website with official tarball for the download (if you do, I will try to include this package officially in easybuild that will simplify the life of other sys-admin for the installation of this code.

isaacovercast commented 4 years ago

Hello Olivier!

When you say "MUSCLE is not indicated in the dependencies" do you mean in the setup.py file? All the required dependencies are in the ipyrad/conda.recipe/meta.yaml file (relative to conda repos naturally). Standard python install mechanisms like pip are not a supported install methods for ipyrad because MUSCLE, samtools and bedtools (among some other dependencies) are not available through pip, unfortunately.

Tarballs for the current version of ipyrad are always available from the github repo, for example: https://github.com/dereneaton/ipyrad/releases/tag/0.9.57

I'm sorry I don't have any experience with easybuild, so I can't offer any advice really on how to streamline this process.

Thank you for working to get ipyrad installed on your local HPC system for your users! Let me know if there's anything further I can do to help!

-isaac

PS - As a former HPC sysadmin myself (converted to a computational biologist) I'm curious about the policy that some HPC sysadmins have of discouraging conda. It seems to me that conda would allow users to manage their own software stacks and free sysadmins from laborious software management duties. I never really understood this conda discouragement, so if you have some thoughts on this I would be grateful to hear your ideas. I want to understand better the motivation behind this.

oliviermattelaer commented 4 years ago

I mean in your documentation: https://ipyrad.readthedocs.io/en/latest/3-installation.html

I have updated the first post with all the external dependencies that I had to install in top of your documentation. But I have it working (and waiting feedback from user)

Cheers,

Olivier

PS: Here is the official document for our (group) of cluster about conda: https://support.ceci-hpc.be/doc/_contents/UsingSoftwareAndLibraries/InstallingSoftwareByYourself/conda.html

isaacovercast commented 4 years ago

Ah yes, I see. Thank you! I have updated the list of dependencies as you have suggested. I pushed the changes, but the docs will update some time "soon", not instantaneously.

Thanks for letting us know!