apps update (#2151)

* Change version from 2.5.1 to 2.5.2. Other minor changes * Minor changes * Minor changes * changed version from 5.30.0 with Bioperl 1.007002 to 5.36.0 with Bioperl 1.007008. Other minor changes * added version 2.5.3. Other minor changes * Minor changes. Also note that the version available on Puhti (1.0.0) is old (updated on 14.08.2019). New version (1.6.0) is available: https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview * Minor changes * Minor changes * added version Python 3.12.3 with Biopython 1.83. Other minor changes * Minor changes * Minor changes * added version 4.6. Other minor changes * added version 23.0.4 on Puhti and 23.0.3 on Mahti. Other minor changes * documention mentions that $DIAMONDDB (/appl/data/bio/biodb/production/diamond) has both Swiss and Trembl uniprot databases. However there is no Trembl database in this location. Please check. * Minor changes * Minor changes * Minor changes * Minor changes * changed version from 0.11.8 to 0.11.9 * added version 1.3.7. Other minor changes * Minor changes * added version 23.9.1 and 24.1.0 on Mahti. Other minor changes * added version 3.4. Other minor changes * VAfter module load biokit, hmmer package is loaded. The variable PFAMDB is set to /appl/soft/bio/interpro/interproscan-5.46-81.0/data/pfam/33.1. However, interproscan-5.46-81.0 does not exist. Please check. * updated link for web manual. Other minor changes * added versions 0.9.85 and 0.9.92. Other minor changes * License not available for version 8.8.2 (this is the default module version) * module name has changed from intel-itac to intel-oneapi-itac. Added version 2021.6.0. Web links updated * Minor changes * Minor changes * Minor changes * changed version from 1.2.8 to 1.2.9. Other minor changes * Minor changes * Mira not available as a package with biokit. Can be loaded as an independent module. Please check * Minor changes * added versions 1.39.5 and 1.44.0. Added link for mothur commands using multiple cores. Other minor chhanges * added links for online manual. Other minor changes * Minor changes * Minor changes * Minor changes * updated user mailing list link. Other minor changes * Minor changes * updated license link. Other minor changes * added links to online manual. Other minor changes * Roary is not available as a package with Prokka mmodule. It can be loaded as an independent module. Please check. * changed version from 9.6 to 9.7. Added version 10.0. Added license link. Other minor changes * changed version from v0.14.1 to v0.14.2. Other minor changes * Minor changes * added version 1.4. Other minor changes * added version 4.0.0. Added link for GitHub repository. Other minor changes * Minor changes * Please check if the link for setting up stacks server on cPouta is correct * updated link for StructureHarvester home page. Other minor changes * Minor changes * Minor changes * added link for GitHub repository page. Other minor changes * added version 1.8. Updated link for home page. Other minor changes * added section on available modules: 3.1.3, 3.3.3 * Minor changes * Minor changes * Minor changes * Minor changes * Update docs/apps/bamtools.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/bioperl.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/bowtie2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/emboss.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/bowtie2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/bs.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/bwa.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/chipster_genomes.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/chipster_genomes.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/edirect.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/edirect.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/exonerate.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/exonerate.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/ipyrad.md Co-authored-by: Ari-Matti Saren <[email protected]> * add mahti to idl * Update docs/apps/ipyrad.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/ipyrad.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/kraken.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/kraken.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/krona.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/krona.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/krona.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/megahit.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/megahit.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/minimap2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/minimap2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/minimap2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/minimap2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/mothur.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/pannzer.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/prokka.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/prokka.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/raxml.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/raxml.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/raxml.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/raxml.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/spades.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/tophat.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/trinity.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/velvet.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/wtdbg2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Update docs/apps/wtdbg2.md Co-authored-by: Ari-Matti Saren <[email protected]> * Replace [email protected] addresses with links to contact page * lots of formatting fixes (empty lines after code etc) --------- Co-authored-by: Ari-Matti Saren <[email protected]> Co-authored-by: Rasmus Kronberg <[email protected]> Co-authored-by: Rasmus Kronberg <[email protected]>
CSCfi · Jul 17, 2024 · a60da03 · a60da03
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diff --git a/docs/apps/alphafold.md b/docs/apps/alphafold.md
@@ -5,7 +5,7 @@ tags:
 
 # AlphaFold
 
-## Description
+
 
 AlphaFold is an AI system developed by [DeepMind](https://www.deepmind.com/) that predicts a protein’s 3D structure from its amino acid sequence.
 
@@ -17,8 +17,6 @@ Free to use and open source under [Apache License 2.0](https://www.apache.org/li
 
 ## Available
 
-### Version on CSC's Servers
-
 -   Puhti: 2.0.1, 2.3.0, 2.3.2-1
 
 

diff --git a/docs/apps/arcgis.md b/docs/apps/arcgis.md
@@ -142,7 +142,7 @@ for it from CSC.
 
 -   Each university has its own ArcGIS contact person, for students and personnel she/he
     is the first point of contact.
--   CSC, GIS-coordinator: [email protected]
+-   CSC, GIS-coordinator: [CSC Service Desk](../support/contact.md)
 -   The technical contact person of the consortium member university has
     the right to contact [Esri-helpdesk] in technical questions.
 
@@ -168,7 +168,7 @@ for it from CSC.
 
 ------------------------------------------------------------------------
 
-## Manual
+## More information
 
 -   [ArcGIS help](https://doc.arcgis.com/en/)
 -   [GIS-analyysimenetelmät ArcGIS 10.2.1 -ohjelmistolla] (Harri

diff --git a/docs/apps/bamtools.md b/docs/apps/bamtools.md
@@ -3,7 +3,7 @@ tags:
   - Free
 ---
 
-# Bamtools
+# BamTools
 
 BamTools provides both a programmer's API and an end-user's toolkit for handling
 BAM files.
@@ -16,39 +16,41 @@ Free to use and open source under [MIT License](https://raw.githubusercontent.co
 
 ## Available
 
--   Puhti: 2.5.1
+-   Puhti: 2.5.2
 -   Chipster graphical user interface
 
-
 ## Usage
 
-In Puhti, Bamtools can be taken in use as a part of biokit module collection:
+On Puhti, BamTools can be taken in use as a part of biokit module collection:
 
 ```bash
 module load biokit
 ```
-The biokit modules sets up a set of commonly used bioinformatics tools. Note however that there are bioinformatics tools in Puhti,
- that have a separate setup commands.
 
-The syntax of bamtools is:
-``` 
-bamtools COMMAND  ARGUMENTS
+The biokit module sets up a set of commonly used bioinformatics tools. Note however that there are other bioinformatics tools on Puhti,
+that have a separate setup commands.
+
+The syntax of BamTools is:
+
 ```
+bamtools COMMAND ARGUMENTS
+```
+
 Available bamtools commands:
 
--  **convert**        Converts between BAM and a number of other formats
--  **count**           Prints number of alignments in BAM file(s)
--  **coverage**        Prints coverage statistics from the input BAM file
--  **filter**          Filters BAM file(s) by user-specified criteria
--  **header**          Prints BAM header information
--  **index**           Generates index for BAM file
--  **merge**           Merge multiple BAM files into single file
--  **random**          Select random alignments from existing BAM file(s), intended more as a testing tool.
--  **resolve**         Resolves paired-end reads (marking the IsProperPair flag as needed)
--  **revert**          Removes duplicate marks and restores original base qualities
--  **sort**            Sorts the BAM file according to some criteria
--  **split**           Splits a BAM file on user-specified property, creating a new BAM output file for each value found
--  **stats**           Prints some basic statistics from input BAM file(s)
+- `convert`         Converts between BAM and a number of other formats
+- `count`           Prints number of alignments in BAM file(s)
+- `coverage`        Prints coverage statistics from the input BAM file
+- `filter`          Filters BAM file(s) by user-specified criteria
+- `header`          Prints BAM header information
+- `index`           Generates index for BAM file
+- `merge`           Merge multiple BAM files into single file
+- `random`          Select random alignments from existing BAM file(s), intended more as a testing tool.
+- `resolve`         Resolves paired-end reads (marking the IsProperPair flag as needed)
+- `revert`          Removes duplicate marks and restores original base qualities
+- `sort`            Sorts the BAM file according to some criteria
+- `split`           Splits a BAM file on user-specified property, creating a new BAM output file for each value found
+- `stats`           Prints some basic statistics from input BAM file(s)
 
 For more information on a specific command, run command:
 
@@ -58,9 +60,8 @@ bamtools help COMMAND
 
 ## Support
 
-[email protected]
-
-## Manual
+[CSC Service Desk](../support/contact.md)
 
-More information about Bamtoos can be found from the [Bamtools home page](https://github.com/pezmaster31/bamtools).
+## More information
 
+More information about BamTools can be found from the [BamTools home page](https://github.com/pezmaster31/bamtools).
diff --git a/docs/apps/bayescan.md b/docs/apps/bayescan.md
@@ -5,8 +5,6 @@ tags:
 
 # BayeScan
 
-## Description
-
 BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies 
 between populations. The analysis is based on the multinomial-Dirichlet model. 
 
@@ -16,29 +14,32 @@ between populations. The analysis is based on the multinomial-Dirichlet model.
 
 Free to use and open source under [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.html)
 
-## Version
+## Available
 
-*   Puhti: 2.1 
+* Puhti: 2.1 
 
 ## Usage
 
 To use BayeScan, first run command
-```text
+
+```bash
 module load biokit
 ```
-After that you can launch bayescan with a command like:
-```text
+
+After that you can launch BayeScan with a command like:
+
+```bash
 bayescan_2.1 -threads 1 test_binary_AFLP.txt 
 ```
 
-With bayescan_2.1 it is important to define the number of threads
-always explisitely. This is because by default BayeScan tries
+With bayescan_2.1, it is important to define the number of threads
+always explicitly. This is because, by default, BayeScan tries
 to use all available cores.
 
-In Puhti, BayeScan tasks should be executed as batch jobs.
+On Puhti, BayeScan tasks should be executed as batch jobs.
 Below is a sample batch job file for BayeScan:
 
-```text
+```bash
 #!/bin/bash
 #SBATCH --job-name=bayescan
 #SBATCH --account=project_XXXXXX
@@ -54,17 +55,18 @@ module load biokit
 bayescan_2.1 -threads ${SLURM_CPUS_PER_TASK} test_binary_AFLP.txt > bayescan_omp.out
 ```
 
-
-The script above reserves 8 hours of computing time, 6GB of memory and 4 computing cores. The XXXXXX in the --account definition
+The script above reserves 8 hours of computing time, 6 GB of memory and 4 computing cores. The `XXXXXX` in the `--account` definition
 should be replaced with the ID number of your computing project. The job can be submitted to the batch job system with command:
-```text
+
+```bash
 sbatch script
 ```
-Don't use BayeScan with more than 8 cores (execpt if you have verified that your task really benefits from larger core numbers).
+
+Don't use BayeScan with more than 8 cores (except if you have verified that your task really benefits from larger core numbers).
 
 More instructions for running batch jobs can be found form [CSC batch job instructions](../computing/running/getting-started.md)
 
 ## More information
 
-*   [BayeScan home page](http://cmpg.unibe.ch/software/BayeScan/index.html)
-*   [BayeScan manual](http://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf)
+* [BayeScan home page](http://cmpg.unibe.ch/software/BayeScan/index.html)
+* [BayeScan manual](http://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf)
diff --git a/docs/apps/bioconda.md b/docs/apps/bioconda.md
@@ -8,7 +8,7 @@ tags:
 !!! error "Bioconda has been deprecated!"
     Bioconda is no longer available on Puhti. Native Conda installations sitting
     directly on the shared file system are ineffective and not recommended in HPC
-    environments like Puhti. Please use [Tykky](../computing/containers/tykky.md)
+    environments such as Puhti. Please use [Tykky](../computing/containers/tykky.md)
     installations instead to wrap your Conda environment within a container. [See
     a tutorial on this here](../support/tutorials/bioconda-tutorial.md). Note that
     some packages that were previously provided through Bioconda are now available

diff --git a/docs/apps/bioperl.md b/docs/apps/bioperl.md
@@ -3,66 +3,60 @@ tags:
   - Free
 ---
 
-# Bioperl
+# BioPerl
 
-
-## Description
-
-Bioperl is a collection of perl modules that facilitate the development of 
-perl scripts for bioinformatics applications. As such, it does not include 
+BioPerl is a collection of Perl modules that facilitate the development of 
+Perl scripts for bioinformatics applications. As such, it does not include 
 ready to use programs in the sense that many commercial packages and free 
-web-based interfaces do. On the other hand, bioperl does provide reusable 
-perl modules that facilitate writing perl scripts for sequence manipulation, 
+web-based interfaces do. On the other hand, BioPerl does provide reusable 
+Perl modules that facilitate writing Perl scripts for sequence manipulation, 
 accessing of databases using a range of data formats and execution and parsing 
-of the results of various molecular biology programs. Consequently, bioperl 
+of the results of various molecular biology programs. Consequently, BioPerl 
 enables developing scripts that can analyze large quantities of sequence 
 data in ways that are typically difficult or impossible with web based systems.
 
-
-
 [TOC]
 
 ## License
-Bioperl is free to use and open source.
-
-BioPerl is licensed under the same terms as Perl itself which is dually-licensed under the terms of the [Perl Artistic license](https://dev.perl.org/licenses/artistic.html) or [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.html).
 
+BioPerl is free to use and open source.
 
+BioPerl is licensed under the same terms as Perl itself which is dually-licensed under the terms of the [Perl Artistic license](https://dev.perl.org/licenses/artistic.html) or [GNU GPLv3](https://www.gnu.org/licenses/gpl-3.0.html).
 
 ## Available
 
--   Puhti: Perl 5.30.0 with Bioperl 1.007002 
-
+- Puhti: Perl 5.36.0 with BioPerl 1.7.8
 
 ## Usage
-In Puhti, bioperl can be taken in use with command:
-```text
+
+On Puhti, BioPerl can be taken in use with the command:
+
+```bash
 module load biokit
 ```
-After this you can launch a bioperl program with command:
-```text
+
+After this, you can launch a BioPerl program with the command:
+
+```bash
 perl my_bioperl_code.pm
 ```
-Alternatively you can change the perl definition in the first line of your code to
-```text
+
+Alternatively you can change the Perl definition in the first line of your code to
+
+```bash
 #!/bin/env perl
 ```
-and execute the perl program:
-```text
-./my_bioperl_code.pm
-```
 
+and execute the Perl program:
 
+```bash
+./my_bioperl_code.pm
+```
 
 ## Support
 
-[email protected]
-
-## Manual
-
-
-*    [Bioperl home page](https://bioperl.org//)
-
-
+[CSC Service Desk](../support/contact.md)
 
+## More information
 
+* [BioPerl home page](https://bioperl.org/)
diff --git a/docs/apps/biopython.md b/docs/apps/biopython.md
@@ -5,10 +5,10 @@ tags:
 
 # Biopython
 
-Biopython is a collection of python modules that facilitate the development of python scripts for 
+Biopython is a collection of Python modules that facilitate the development of Python scripts for 
 bioinformatics applications. As such, it does not include ready to use programs in the sense that 
 many commercial packages and free web-based interfaces do. On the other hand, Biopython provides 
-reusable python modules that facilitate writing scripts for sequence manipulation, accessing of 
+reusable Python modules that facilitate writing scripts for sequence manipulation, accessing of 
 databases using a range of data formats and execution and parsing of the results of various 
 molecular biology programs. Consequently, Biopython enables developing scripts that can analyze 
 large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
@@ -21,42 +21,45 @@ Biopython is free to use and open source. It is dual licensed under [Biopython L
 
 ## Available
 
--   Puhti: Python 3.10.6 with Biopython 1.79
+- Puhti: Python 3.10.6 with Biopython 1.79
+- Puhti: Python 3.12.3 with Biopython 1.83
 
-In Puhti, Biopython libraries, as well as many other bioinformatics related Python libraries are available.
+On Puhti, Biopython libraries, as well as many other bioinformatics-related Python libraries are available.
 
-```text
+```bash
 module load biopythontools
 ```
 
-When the module is loaded, you can launch a biopython program with command:
-```text
+When the module is loaded, you can launch a Biopython program with the command:
+
+```bash
 python my_biopython_code.py
 ```
-Alternatively you can change the python definition in the first line of your code to
-```text
+
+Alternatively, you can change the python definition in the first line of your code to
+
+```bash
 #!/bin/env python
 ```
 
 and execute the python program
 
-```text
+```bash
 ./my_biopython_code.pm
 ```
 
 New python libraries can be installed with `pip install` command.
-For example, Python library called OBITools3 could be installed with command:
+For example, a Python library called OBITools3 could be installed with the command:
 
-```text
+```bash
 pip install --user OBITools3
 ```
 
-Further instructions on how to set the installation location etc can be found in the general
-[Python](python.md) page.
-
-## Manual
+Further instructions on how to set the installation location etc. can be found in the
+[CSC Python usage guide](../support/tutorials/python-usage-guide.md).
 
-More information about biopython can be found form the homepage of biopython.
+## More information
 
-*  [www.biopython.org](http://www.biopython.org)
+More information about Biopython can be found form the homepage of Biopython.
 
+* [www.biopython.org](https://biopython.org/)