182023-04-25 11:43:41fhoma172023-04-25 11:29:29fhoma162023-04-25 09:53:47fhoma152021-10-29 14:53:21fhoma142021-10-29 14:35:37fhoma132021-10-29 14:22:07fhoma122021-10-29 14:12:19fhoma112021-10-29 09:34:51fhoma102020-05-13 10:51:13fhomamonitor jobs92020-04-27 07:40:01fhoma82020-04-27 07:39:27fhomaCompiling software72020-04-26 08:25:10fhoma62020-04-26 08:23:34fhoma52020-04-26 08:22:34fhoma42020-04-26 08:22:05fhoma32020-04-26 07:54:20fhomaminiconda22020-04-26 06:25:46fhomaAdd nav menu12020-04-24 07:21:07fhomaR packages

Installing software or pipeline can be a difficult task to accomplish. Therefore we suggest all users to make the programs they installed available to all users whenever it is possible. In general programs/pipelines that should be available to all are installed in /tools folder. On this page will be described how to make tools available on our system for installation procedure of your specific program please refer to the instructions coming with that program.

In principle any users except students and guests should be able to install bioinfo tools in folders made for that purpose.

We do ask users to provide test data for all install software. This way it becomes easy to check whether a software works or not. It is also good to define default command to test a tool, see next section to know more about this.

Installing software on potato can be separated into 3 parts: Compiling/generating binaries (/tools/software/bioinfo-tools) Adding binaries and libraries to the path (/tools/modulefiles) Adding test data (/tools/test_data)

The following scheme will help you understanding how tools should be placed in /tools/software/bioinfo-tools/ /tools/software/bioinfo-tools/<category_name>/<generic_name>/<version_name>/ CATEGORY NAMEEvery tool is place in a specific category, users have to choose which category is adequate for there tool. If no category is suited for the new tool, make a new folder. GENERIC NAMEThis the name of the tool without any version information VERSION NAMEThis the tool's name and the version or simply the version an example for assembly tools could look like this,

Once the binaries has been placed in software folder, the next step is to add the path to modules. By doing so users can easily load the software using the command module. For each software installed a module file should be created, users module files are located in /tools/modulefiles. Make a new file following this scheme, /tools/modulefiles/<TOOL_NAME>/<VERSION> Here is a test module file that you can modify to suit your case, version "]]> "]]> "]]> "]]> "]]> "]]> ]]> ]]> ]]> ]]> ]]> "]]>

We kindly as all users to provide test data for all software they install as we as a basic command to run the a test (cf. module file). Test data should be a very tiny (simulated or not) amount of data to use to test a tool, a test run should last less than 5min.Make a folder for your tool in /tools/test_data/<TOOL> then add your data and a "sbatch" file to run the test.

Anaconda (or Conda) is a well known program for managing environments and packages. It is very popular inn bioinformatics as it allows users with little experience to easily install needed tools and all dependencies. It also makes it easy for users to load the specific environments they need without modifying their bashrc themselves. On this server you will find 2 versions of miniconda installed, miniconda3 for python 3 and miniconda2 for python 2.7 environments. Conda's users guide can be found here, . Load conda module and set needed for conda to work. Be aware that this process rebase you default python bin folder into conda base folder. You can see all available environments To make it easy for all users to locate needed environments, use descriptive names when making new environments, eg. software-exact_version_number. Activate an existing environment ]]> Deactivate the current environment Load 2 conda environments (we do not recommend doing this as it may lead to big confusions) Nested environment ]]> Create new conda environment, there are 2 ways of doing this from scratch or from a YAML config file. The latter one will create the environment and install all listed software You can also give a list of software and versions when installing from scratch Replace <env_name>, with a descriptive name. ]]> ]]> ]]> ]]> Remove an unused environment ]]> --all]]>

Packages for R are installed within R, so to install R packages, you will first need to load the module R and run R. Use the following R command to print where are the R libraries. Users libraries are installed in /tools/R_libs/3.6.1 To see all available/installed packages To install R packages and dependancies. Installation will automatically be done in a /tools/R_libs/3.6.1 if permissions allows it. If not you could be asked to create a private one. "]]>,..."]]> To install BIOINFORMATICS R PACKAGES, we recommend to use "bioconductor" channels. "]]>"]]> Read more about R and bioconductor:

Computers description Request an account storage description First login Receiving sequencing data transferring data Submitting jobs Monitor jobs Install tools Space management #top