This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Unable to load bioinfo_tools module on linux bash

Hi,

I have seen in several bash scripts that the following module is used:

bioinfo-tools

However, when I try to look up for it using the spider command and load it, my system is unable to do so:

module spider bioinfo-tools
Lmod has detected the following error:  Unable to find: "bioinfo-tools".

module load bioinfo-tools
Lmod has detected the following error:  The following module(s) are unknown: "bioinfo-tools"

Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
  $ module --ignore_cache load "bioinfo-tools"

Also make sure that all modulefiles written in TCL start with the string #%Module

Did anyone came across such an issue with the bioinfo-tools module and could help me with that issue?

Many thanks!

bash linux
• 2,076 views • link
updated by Ram Ram • written by barzilayrom1 • barzilayrom1

2 answers

Modules are environment-specific. You have to talk to the person admining that machine/cluster/HPC.

• 0 views • link
written by ATpoint ATpoint

Many thanks for the response, truly appreciate it!

As you suggested, I did contact the admin of the cluster in order to install that module.

However, as GenoMax mentioned, I also suspect that the bioinfo-tools is a sort of catch-all name for several bioinformatics programs. Therefore, while waiting for reply from my cluster admin, I tried to search the web to find out which programs are included within this module, but unfortunately found only few scripts that use it, without any further explanation about what it is or what it includes. Would love to hear if you have any suggestions for finding any additional information in that case.

Thanks again!

• 0 views • link
written by barzilayrom1 • barzilayrom1

As I said, a module is something specific to your cluster. It has the name that the admin gives it so you cannot google this. They could have also named this coolio_bioinfo_toolies or anything else. It is a custom thing. You can simply use conda to install whatever tools you need independent of the module system.

• 0 views • link
written by ATpoint ATpoint

If your cluster/system uses module system then that module is missing on your server. Admins generally control modules so you will need to talk with them to go about getting this installed.

That said bioinfo-tools sounds like a catch-all name for many programs that may be loaded via a single module so you will need to know which programs are in this module to get them installed.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this