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How to search for software

There are thousands of packages installed at MetaCentrum. The list of selected software is by far not complete.

In general, when searching for an application, you should checklist the following:

  1. Look at the list of selected software either sorted alphabetically or by field of interest.
  2. Use module avail command as described on this page.
  3. Go through software prepared as containers.

Tip

No luck? The consult how to install new (version of) software either locally or system-wide.

Modules

To search for any package, use command module avail PACKAGE_NAME.

Search is case-insensitive

For example, module avail r/ and module avail R/ are the same for the purpose of searching. Other commands, however (such as module add or module load) are case-sensitive.

You can use stars (with backslash or quotes)

The module avail command accepts bash special characters. The most useful is the * which replaces any string; for example module avail g\*, module avail 'g*', module avail "g*" lists all modules beginning with "g".

Why backslash or quotes?

To make it to module avail, the * must be protected by backslash or quotes not to be expanded by shell. To experiment with this behaviour, try touch g001; module avail g* (returns nothing) versus touch g001; module avail g\* (returns list of modules).

Example 1: Orca versions

(BULLSEYE)user123@skirit:~$ module avail or
----------- /packages/run/modules-5/debian11avx512 ---------------
orca/  orthofinder/  

Key:
modulepath  directory/
The above search will return all modules starting with the string "or".

(BULLSEYE)user123@skirit:~$ module avail orca
----------- /packages/run/modules-5/debian11avx512 ---------------
orca/  

Key:
modulepath  directory/
The above search is limited only to "orca" package, but does not show versions.

(BULLSEYE)user123@skirit:~$ module avail orca/
----------- /packages/run/modules-5/debian11avx512 ---------------
orca/2.6.4  orca/3.0.1  orca/4.0.2  orca/4.1.1  orca/4.1.2  orca/4.2.0  orca/4.2.1  orca/5.0.1-intel-19.0.4-bnofsgq  orca/5.0.3-intel-19.0.4-dyfxe2x  

Key:
modulepath
With "/" at the end, the search will output all versions available for the specified module.

Example 2: R package

Modulefiles of system-wide installed R package are of the form r-PACKAGE.

To list all R packages, run

module avail r-*

Let's say you want to use package bsgenome. Commands

module avail bsgenome
module avail bsgenome*

will yield nothing.

On the other hand,

module avail *bsgenome*

will show up the package.

Containers

A minor part of software is prepared as Singularity containers.

You can list them at

ls /cvmfs/singularity.metacentrum.cz/

For instructions on container usage, see the containers chapter.

Services

There are a number of services closely connected to MetaCentrum which may offer the software you need, too.