client_CLI_usage.md
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@@ -8,221 +8,206 @@ For information on how to run software from the BioGrids collection and configur
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### General
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The BioGrids software installation client is a command line-based installer for the BioGrids software collection. The application allows for selected applications to be installed in the familiar BioGrids environment.
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-The client displays software 'Collections' as a list.
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+To get started, load the BioGrids environment :
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- $ sbgrid list
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+ $ source /programs/biogrids.shrc
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```
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-Crystallography
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- 3dna
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- adxv
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- albula
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- autoproc
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- ...
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-
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-NMR
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- aqua
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- aria
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- cara
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- ccpnmr
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- ccpnmr-chembuild
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- ...
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-
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-Electron Microscopy
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- 2dx
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- ace2
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- auto3dem
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- bfactor
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- bsoft
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- burnham-brandeis-helical-package
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- chimera
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- ...
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-
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-Structure Visualization & Analysis
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- 3dna
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- anaconda
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- apbs
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- aqua
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- bobscript
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- caver
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- caver-analyst
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- ccp4mg
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- chimera
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- ...
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-
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-Computational Chemistry
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- ambertools
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- apbs
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- appion
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- autodock
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- autodock-vina
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- avogadro
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- concoord
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- dock
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- gromacs
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- ...
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-
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-Other
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- a2ps
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- abyss
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- aline
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- amigos-ii
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- amps
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- assemble2
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- bamtools
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- ...
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+********************************************************************************
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+ Software Support by BioGrids
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+********************************************************************************
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+ Developed with support from HMS Tools-and-Technologies fund.
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+ If your use of BioGrids compiled software was an important element in
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+ your publication, please include the following statement in your work:
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+ "Software used in the project was installed and configured by BioGrids
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+ (cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
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+********************************************************************************
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+This BioGrids installation last updated: 2017-10-11
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+ Please submit bug reports and help requests to: help@biogrids.org.
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+********************************************************************************
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+ Capsule Status: Active
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+ For additional information visit https://sbgrid.org/wiki/capsules
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+******************************************************************
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```
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-Information about each title, including a description and links to documentation can be show with the *sbgrid info <title>* command.
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-### Example : Installing Albula
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+The client displays software 'Collections' as a list.
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- $ sbgrid info albula
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+ $ biogrids list
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```
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-Package: ALBULA
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-Name : albula
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-
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-Available versions:
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-* 3.2.0-2 (default)
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-* 3.1.0-13
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-* 3.0.0-14
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-* 2.2.12
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+-- High-Throughput Sequencing -----------------------------------------------------------------
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+abyss blat diamond miso solexaqaplusplus
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+bamtools bowtie ebseq mothur spades
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+bcftools bowtie-2 edger picard sra-toolkit
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+bedtools breseq fasta pysam star
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+bigpre bwa fastqc quartz tophat
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+bioawk cora hisat2 rsem trimmomatic
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+biobambam2 cufflinks kallisto sailfish gorpipe
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+blast cutadapt macs2 salmon
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+blastplus deseq2 mica samtools
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+-- Genomics -----------------------------------------------------------------------------------
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+bedtools ffp mrbayes sam sra-toolkit
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+bioawk infernal plink solexaqaplusplus
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+-- Proteomics ---------------------------------------------------------------------------------
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+amps mafft modeller rosetta zdock
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+-- Visualization ------------------------------------------------------------------------------
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+aline cytoscape igv pymol-open-source weblogo
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+-- Other --------------------------------------------------------------------------------------
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+a2ps cython miso python
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+anaconda emboss mono pytz
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+biogrids-installer fasta mpich qt
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+blast ghostscript numpy r
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+blastplus globus-connect-personal pandas rstudio
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+breseq mafft perl tex-live
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+```
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-Collection(s): Crystallography
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+Information about each title, including a description and links to documentation can be shown with the *biogrids info <title>* command.
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-Description:
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- consists of the standalone program ALBULA VIEWER, a fast and easy-to-
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-use program that allows optimal visualization of PILATUS and EIGER data,
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-and ALBULA API, a Python programming interface for displaying images and
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-performing operations and calculations. The API enables you to easily
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-integrate the viewer functionality into your beamline infrastructure or
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-experimental setup.
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+### Example : Installing samtools
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-Links:
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-* Website: https://www.dectris.com/Albula_Overview.html
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```
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+$ ./biogrids info samtools
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-To install:
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+Package: SAMtools
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+Name slug: samtools
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- $ sbgrid install albula
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+Available versions:
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+ * 0.1.19
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+ * 1.3
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+ * 1.3.1
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+ * 1.4.1
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+ * 1.5 (default)
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-```
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-Installing: albula
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-Updating installation configuration...
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-Installation was successfull!
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-```
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+Grids(s): Biogrids
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+Collection(s): High-Throughput Sequencing
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-To get started, load the BioGrids environment :
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+Description:
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+ (Sequence Alignment/Map) a generic format for storing large nucleotide
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+sequence alignments that provides various utilities for manipulating
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+alignments, including sorting, merging, indexing and generating alignments
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+in a per-position format.
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- $ source /programs/sbgrid.shrc
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+Links:
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+ Website: http://www.htslib.org/
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+ Manual: http://www.htslib.org/doc/samtools.html
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+ Forum help: https://lists.sourceforge.net/lists/listinfo/samtools-help```
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+To install:
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```
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- Software Support by BioGrids (www.sbgrid.org)
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-********************************************************************************
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+$ biogrids install samtools
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-...
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+samtools@1.5 for i386-mac installed
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+Updating installation configuration...
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-BioGrids installation last updated: 2016-10-21
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-Please submit bug reports and help requests to: <bugs@sbgrid.org> or
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- <http://sbgrid.org/bugs>
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-********************************************************************************
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```
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-### Example : Removing Albula
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- $ sbgrid remove albula
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+### Example : Removing samtools
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+
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+ $ biogrids remove samtools
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results in :
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```
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-Removing: albula
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+Package samtools removed.
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Updating installation configuration...
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-Package removed!
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```
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### Version selection
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-Default versions are installed by default for each application, though individual versions can be selected for each title.
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+Default versions are installed for each application. BioGrids makes available several versions for each software package. You can install specific versions if needed.
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-To do so, include the version after the title followed the version. To see what versions are available, use the *sbgrid info <title>* command. Let;s us the title epmr as an example here:
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+To do so, specify the version after the title name with an @ symbol. Use the *biogrids info <title>* command to see all available versions.
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- $ sbgrid info epmr
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+ $ biogrids info samtools
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```
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-Package: EPMR
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-Name slug: epmr
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+Package: SAMtools
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+Name slug: samtools
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Available versions:
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-* 16.04 (default)
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-* 16.01
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-* 15.12
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-* 15.04
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-* 13.07
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-* 11.02
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+ * 0.1.19
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+ * 1.3
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+ * 1.3.1
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+ * 1.4.1
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+ * 1.5 (default)
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-Collection(s): Crystallography
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+Grids(s): Biogrids
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+Collection(s): High-Throughput Sequencing
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Description:
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- a program that finds crystallographic molecular replacement solutions
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-using an evolutionary search algorithm. The program directly optimizes
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-three rotational and three positional parameters for the search model with
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-respect to the correlation coefficient between Fo and Fc.
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+ (Sequence Alignment/Map) a generic format for storing large nucleotide
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+sequence alignments that provides various utilities for manipulating
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+alignments, including sorting, merging, indexing and generating alignments
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+in a per-position format.
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Links:
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-* Website: http://www.epmr.info/
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-* Manual: http://www.epmr.info/UsersGuide.html
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-```
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+ Website: http://www.htslib.org/
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+ Manual: http://www.htslib.org/doc/samtools.html
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+ Forum help: https://lists.sourceforge.net/lists/listinfo/samtools-help
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+ ```
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-To install version 11.02, add the version string like so:
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+To install samtools version 1.4.1, add the version string like so:
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- $ sbgrid install epmr 11.02
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+ $ biogrids install samtools@1.4.1
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which will produce :
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```
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-Installing: epmr (11.02)
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-Updating installation configuration...
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-Installation was successfull!
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-key@key-mbp [20161021-21:05:56] ~/Downloads
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+samtools@1.4.1 for i386-mac installed
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+Updating installation configuration..
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```
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-Check which versions are installed with the sbgrid info command again
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+Check which versions are installed with the biogrids info command again
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- $ sbgrid info epmr
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+ $ biogrids info samtools
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```
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-epPackage: EPMR
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-Name slug: epmr
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+Package: SAMtools
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+Name slug: samtools
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Available versions:
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-* 16.04 (default)
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-* 16.01
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-* 15.12
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-* 15.04
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-* 13.07
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-* 11.02 (installed)
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+ * 0.1.19
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+ * 1.3
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+ * 1.3.1
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+ * 1.4.1 (installed)
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+ * 1.5 (default)
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-...
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+Grids(s): Biogrids
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+Collection(s): High-Throughput Sequencing
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-```
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+Description:
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+ (Sequence Alignment/Map) a generic format for storing large nucleotide
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+sequence alignments that provides various utilities for manipulating
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+alignments, including sorting, merging, indexing and generating alignments
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+in a per-position format.
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+
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+Links:
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+ Website: http://www.htslib.org/
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+ Manual: http://www.htslib.org/doc/samtools.html
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+ Forum help: https://lists.sourceforge.net/lists/listinfo/samtools-help```
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+
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+Reload the biogrids shell to use the new version ( or set the environment variable SAMTOOLS_M=1.4.1 ).
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+
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+ $ source /programs/biogrids.shrc
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Confirm with the *sbwhich* command
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- $ sbwhich epmr
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+ $ sbwhich samtools
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```
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-/programs/i386-mac/epmr/11.02/epmr
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+/programs/i386-mac/samtools/1.5/bin/samtools
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```
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-Reload the sbgrid shell to use the new version ( or set the environment variable EPMR_M=11.02 ).
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-### Software Versions Management in the BioGrids environment
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+
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+### Software Version Management in the BioGrids environment
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If you have a single version of an application installed, explicit version selection in your environment is not needed.
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In the case of multiple installed versions, the *BioGrids Default* version will be the version available at the terminal when it is installed, unless configured otherwise in *~/.sbgrid.conf*.
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-In the case of multiple non-default versions installed, the *latest release* will be version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file. This is the same as in the standard BioGrids environment.
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+In the case of multiple non-default versions installed, the *latest release* will be the version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your *~/.sbgrid.conf* file. This is the same as in the standard BioGrids environment.
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**Version priority in the shell**
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1. *~/.sbgrid.conf*
... ...
@@ -236,18 +221,18 @@ There is more info on how to do that here --> [BioGrids version overrides](vers
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To use the software at the terminal in bash, open a new terminal and run
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- $ source /programs/sbgrid.shrc
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+ $ source /programs/biogrids.shrc
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or in tcsh
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- $ source /programs/sbgrid.cshrc
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+ $ source /programs/biogrids.cshrc
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### Questions, Problems and Known Issues
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-For questions or problems, the Help menu will direct to the BioGrids help page. Or just email *bugs@sbgrid.org*.
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-If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/sbgrid.log file with your report.
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+For questions or problems, the Help menu will direct you to the BioGrids help page. Or just email *help@biogrids.org*.
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+If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/biogrids.log file with your report.
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**Known issues**
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* The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.
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-* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/sbgrid.
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+* In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/biogrids.