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update HPCBIOS_2012-94
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Signed-off-by: Fotis Georgatos <[email protected]>
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fgeorgatos committed Jul 25, 2015
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30 changes: 15 additions & 15 deletions HPCBIOS_2012-94.rst
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Expand Up @@ -28,7 +28,7 @@ productivity environment across any HPCBIOS resources:
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **Cython** | 0.16 | MUST | http://pypi.python.org/pypi/Cython/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **R language** | v2.14.2 or v2.15.x | MUST | http://www.r-project.org |
| **R language** | v2.14.2 or v3.2.x or later | SHOULD | http://www.r-project.org |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **Bioconductor** | v2.10 | SHOULD | http://www.bioconductor.org |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
Expand Down Expand Up @@ -168,6 +168,20 @@ productivity environment across any HPCBIOS resources:
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **Trinity** | 2013-02-25 | MUST | http://trinityrnaseq.sourceforge.net/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **IDBA-UD** | 1.1.1 | SHOULD | http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **Ruby** | v1.9.3-p194 or later | SHOULD | http://www.python.org/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **HOMER** | 4.2 | SHOULD | http://homer.salk.edu/homer/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **PhyML** | latest | SHOULD | http://www.atgc-montpellier.fr/phyml/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **Clustal** | latest | SHOULD | http://www.clustal.org/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **PyMOL** | latest | SHOULD | http://pymol.sf.net/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| **FastQC** | 0.10.0 | SHOULD | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+



Expand All @@ -186,12 +200,8 @@ Future potential candidates for this policy:
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| mr-mpi-blast | latest | SHOULD | https://github.com/andreyto/mr-mpi-blast |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| Ruby | v1.9.3-p194 or later | SHOULD | http://www.python.org/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| BioRuby | latest | SHOULD | http://bioruby.org |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| IDBA-UD | 1.0.9 | SHOULD | http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| PolyPhen-2 | 2.2.2r405 | SHOULD | http://genetics.bwh.harvard.edu/pph2/dokuwiki/start |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| SSAHA | 31c | SHOULD | http://www.sanger.ac.uk/resources/software/ssaha/ |
Expand Down Expand Up @@ -226,28 +236,18 @@ Future potential candidates for this policy:
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| nesoni | latest | SHOULD | http://bioinformatics.net.au/software.nesoni.shtml |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| PhyML | latest | SHOULD | http://www.atgc-montpellier.fr/phyml/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| galaxy | >ca0c4ad2bb39 | SHOULD | http://galaxy.psu.edu/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| swarm | latest | SHOULD | http://biowulf.nih.gov/apps/swarm.html /download/swarm.tar |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| WU-BLAST | latest | SHOULD | http://blast.wustl.edu/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| Clustal | latest | SHOULD | http://www.clustal.org/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| PAUP | latest | SHOULD | http://paup.csit.fsu.edu/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| PHYLIP | latest | SHOULD | http://evolution.genetics.washington.edu/phylip.html |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| PyMOL | latest | SHOULD | http://pymol.sf.net/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| FastQC | 0.10.0 | SHOULD | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| QuEST | 2.4 | SHOULD | http://mendel.stanford.edu/sidowlab/downloads/quest/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+
| HOMER | 4.2 | SHOULD | http://homer.salk.edu/homer/ |
+----------------------------------------+-----------------------------+--------------------+------------------------------------------------------------+

This productivity environment will be supplemented with other related
productivity tools as they become available on allocated systems.
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