Difference between revisions of "Biotin2.hpc.uio.no"
(→Live computational resource usage information (cpu and memory) - Biotin3) |
|||
(60 intermediate revisions by 4 users not shown) | |||
Line 1: | Line 1: | ||
− | == | + | |
+ | <code>biotin2</code> is a departmental general use server for the "in silico" groups. | ||
+ | |||
+ | <code>biotin3</code> is the Mathelier group server for its exclusive use. | ||
+ | |||
+ | = Description of the biotin[2,3].hpc.uio.no servers and associated VMs with replicated applications = | ||
+ | |||
+ | * biotin2: 128 [https://ark.intel.com/products/84680/Intel-Xeon-Processor-E7-8860-v3-40M-Cache-2-20-GHz- Intel Haswell cores], 1 Tb RAM, 162 Tb of local disk space allocated for various NCMM groups | ||
+ | * biotin3: 192 [https://ark.intel.com/products/96900/Intel-Xeon-Processor-E7-8894-v4-60M-Cache-2-40-GHz- Intel Broadwell cores], 1 Tb RAM, 5 Tb of local disk space allocated as scratch and local partitions for the Mathelier Group. | ||
+ | * kuijjer2: 24 [https://www.amd.com/en/products/cpu/amd-epyc-7601 AMD EPYC virtual cores], 128 Gb RAM, 5 Tb of local disk space for the Kuijjer Group | ||
+ | * waszak1: 48 [https://www.amd.com/en/products/cpu/amd-epyc-7601 AMD EPYC virtual cores], 128 Gb RAM, 4 Tb of local disk space for the Waszak Group | ||
+ | |||
+ | == List of software installed on the biotin[2,3].hpc.uio.no servers and VMs == | ||
{| class="wikitable" style="text-align: center;" | {| class="wikitable" style="text-align: center;" | ||
|- | |- | ||
− | | '''Application''' || '''Version on biotin2.hpc.uio.no and biotin3.hpc.uio.no''' || '''Status''' || '''Comments''' || | + | | '''Application''' || style="width: 250pt" | '''Version on biotin2.hpc.uio.no and biotin3.hpc.uio.no''' || '''Status''' || '''Comments''' || |
|- | |- | ||
− | | [https://se.mathworks.com/products/matlab.html?s_tid=hp_fp_ml MATLAB] || | + | | [https://se.mathworks.com/products/matlab.html?s_tid=hp_fp_ml MATLAB] || R2019b (9.7.0.1216025) 64-bit (glnxa64) || Done || University of Oslo Site License || |
|- | |- | ||
− | | [https://www.r-project.org/ R] with [https://www.bioconductor.org/ Bioconductor] || R version 3.5.1 (2018-07-02) -- " | + | | [https://www.r-project.org/ R] with [https://www.bioconductor.org/ Bioconductor] || R version 3.5.1 (2018-07-02) "Feather Spray" (3.5.1 is not in active maintenance )<br> R version 3.6.1 (2019-07-05) "Action of the Toes" |
+ | R version 4.0.2 (2020-04-02) "Taking Off Again"<br>see also <code>'''module list'''</code> | ||
+ | | Done || To access R v. 3.6.1, type: | ||
+ | - <code>'''module load R/3.6.1'''</code> | ||
+ | |||
+ | To access R v. 4.0.2, type: | ||
+ | |||
+ | - <code>'''module load R/4.0.2'''</code> | ||
+ | | | ||
|- | |- | ||
| [https://www.perl.org/ Perl] || v5.16.3 || Done || Upgraded version should not cause any problems || | | [https://www.perl.org/ Perl] || v5.16.3 || Done || Upgraded version should not cause any problems || | ||
Line 13: | Line 33: | ||
| [https://perl6.org/ Perl 6] || 6c || Done || Based on Rakudo Star release 17.4 || | | [https://perl6.org/ Perl 6] || 6c || Done || Based on Rakudo Star release 17.4 || | ||
|- | |- | ||
− | | [https://www.python.org/ Python] || Python 2.7.5 | + | | [https://www.python.org/ Python] || Python 2.7.5, as well as 3,4,2, 3.5.1, 3.6.9 and 3.8.0 from RedHat Software Collections plus installed scientific computing modules. For a list of Python modules we maintain, please visit [[this page]]. || Done || To access the default Python 2.7 environment, you need to type nothing. |
+ | '''Please note the [https://pythonclock.org/ End Of Life (EOL) of Python 2.7.x] . Make an effort to use Python 3.x instead, as described below.''' | ||
+ | |||
+ | To enable the Python 3 version, please type on your shell | ||
+ | |||
+ | -For version 3.4.2: | ||
+ | |||
+ | <code>'''scl enable rh-python34 bash'''</code> | ||
+ | |||
+ | -For version 3.5.1: | ||
+ | |||
+ | <code>'''scl enable rh-python35 bash'''</code> | ||
+ | |||
+ | -For version 3.6.9: | ||
+ | |||
+ | <code>'''scl enable rh-python36 bash'''</code> | ||
+ | |||
+ | -For version 3.8.0: | ||
+ | |||
+ | <code>'''scl enable rh-python38 bash'''</code> | ||
+ | |||
+ | | | ||
|- | |- | ||
| [https://github.com/ParkerLab/ataqv ataqv] || 1.0.0 || Done || ataqv was built against the HTSLIB in /lsc/htslib and with gcc 8.2.1 (devtoolset-8) || | | [https://github.com/ParkerLab/ataqv ataqv] || 1.0.0 || Done || ataqv was built against the HTSLIB in /lsc/htslib and with gcc 8.2.1 (devtoolset-8) || | ||
+ | |- | ||
+ | |[https://github.com/BradnerLab/pipeline/wiki/bamliquidator bamliquidator] | ||
+ | |Latest commit c2c4865, Oct 3, 2017 | ||
+ | |Done | ||
+ | |Compiled against HDF5 lib version 1.8.22 | ||
+ | | | ||
+ | |- | ||
+ | |[https://bitbucket.org/bgframework/bgsignature/src/master/ BGSignature] | ||
+ | |0.2 | ||
+ | |Done | ||
+ | |Installed with Python 3.6, so to use it, do a: | ||
+ | '''scl enable rh-python36 bash''' | ||
+ | | | ||
|- | |- | ||
| [https://github.com/wassermanlab/BiasAway BiasAway] || norpy version || Done || - || | | [https://github.com/wassermanlab/BiasAway BiasAway] || norpy version || Done || - || | ||
Line 27: | Line 81: | ||
| [https://bedops.readthedocs.io/en/latest/ bedops] || version 2.4.14 || Done || - || | | [https://bedops.readthedocs.io/en/latest/ bedops] || version 2.4.14 || Done || - || | ||
|- | |- | ||
− | | [https://bitbucket.org/cegx-bfx/cegx_bsexpress bsExpress] || v0.5cegx || Done || The sofware was modified/fixed to run properly on our production environment. Patches are described in [https://rt.uio.no/Ticket/Display.html?id=2444978 | + | | [https://bitbucket.org/cegx-bfx/cegx_bsexpress bsExpress] || v0.5cegx || Done || The sofware was modified/fixed to run properly on our production environment. Patches are described in [https://rt.uio.no/Ticket/Display.html?id=2444978 UiO RT case #2444978]. || |
|- | |- | ||
| [https://code.google.com/archive/p/bsmap/ bsmap] || version 2.74 || Done || - || | | [https://code.google.com/archive/p/bsmap/ bsmap] || version 2.74 || Done || - || | ||
Line 39: | Line 93: | ||
| [https://github.com/ParkerLab/cta cta] || 0.1.2 || Done || Compiled with gcc 8.2.1 (devtoolset-8). It does not compile gcc 4.x . || | | [https://github.com/ParkerLab/cta cta] || 0.1.2 || Done || Compiled with gcc 8.2.1 (devtoolset-8). It does not compile gcc 4.x . || | ||
|- | |- | ||
− | | [https://www.gnu.org/software/datamash/ datamash] || | + | | [https://www.cgl.ucsf.edu/chimera/ chimera] || 1.15 || Done || - . || |
+ | |- | ||
+ | | [https://www.gnu.org/software/datamash/ datamash] || 1.1.1 || Done || - || | ||
+ | |- | ||
+ | | [https://cryoem.bcm.edu/cryoem/downloads/view_eman2_version/30 eman] || 2.31 || Done || source /lsc/eman/2.31/etc/profile.d/conda.sh WARNING: PYTHONPATH set, might interfere with eman2|| | ||
|- | |- | ||
| [https://github.com/amathelier/DNAshapedTFBS DNAshapedTFBS] || Latest commit 418fff6 on 28 Sep 2016 || Done || - || | | [https://github.com/amathelier/DNAshapedTFBS DNAshapedTFBS] || Latest commit 418fff6 on 28 Sep 2016 || Done || - || | ||
Line 54: | Line 112: | ||
|- | |- | ||
| [https://gcc.gnu.org/gcc-7/changes.html gcc 7 compiler] || v7.3.1 || Done || Default compiler for RHEL 7 is gcc 4.8.x. We include as well gcc version 7. To use type at your shell prompt: <code>scl enable devtoolset-7 bash</code> || | | [https://gcc.gnu.org/gcc-7/changes.html gcc 7 compiler] || v7.3.1 || Done || Default compiler for RHEL 7 is gcc 4.8.x. We include as well gcc version 7. To use type at your shell prompt: <code>scl enable devtoolset-7 bash</code> || | ||
+ | |- | ||
+ | |[https://gcc.gnu.org/gcc-8/ gcc 8 compiler] | ||
+ | |v8.2.1 | ||
+ | |Done | ||
+ | |To use type at your shell prompt: <code>scl enable devtoolset-8 bash</code> | ||
+ | | | ||
|- | |- | ||
| [https://github.com/ExpressionAnalysis/ea-utils Expression analysis ea-utils] || github repo 31/10/2017 || Done || - || | | [https://github.com/ExpressionAnalysis/ea-utils Expression analysis ea-utils] || github repo 31/10/2017 || Done || - || | ||
Line 67: | Line 131: | ||
| [http://homer.ucsd.edu/homer/ Homer Tools] || v4.7.2 || Done || Configurable by the end users, installed genomes hg(17-19),mm(8-10),xenTro(2,3),ce(6,10),danRer7, galGal4,rn5 || | | [http://homer.ucsd.edu/homer/ Homer Tools] || v4.7.2 || Done || Configurable by the end users, installed genomes hg(17-19),mm(8-10),xenTro(2,3),ce(6,10),danRer7, galGal4,rn5 || | ||
|- | |- | ||
− | | meme | + | | [http://meme-suite.org/doc/download.html?man_type=web meme] || v.4.11.4 || Done || No sequence databases were downloaded on biotin, hence no databases on biotin2 || |
+ | |- | ||
+ | | [https://www.tbi.univie.ac.at/RNA/ ViennaRNA] || v2.1.9 || Done || - || | ||
+ | |- | ||
+ | | [http://fureylab.web.unc.edu/software/fseq/ F-Seq] || v1.8.4 || Done || In biotin2 we have JAVAOPTS="-Xmx16000M" as opposed to JAVAOPTS="-Xmx8000M" of biotin (twice the heap size) configued in fseq || | ||
+ | |- | ||
+ | | [https://www.cs.waikato.ac.nz/ml/weka/downloading.html WEKA] || v3.7.13 || Done || Type <code>launch_weka</code> to start the GUI of the program. Check the functionality against Java 1.8 . Heap size is set to 4 Gig. (4 x biotin size) || | ||
+ | |- | ||
+ | | [http://software.broadinstitute.org/software/igv/ IGV] || v2.3.88 || Done || Type <code>igv.sh</code> to start the browser. Expect long startup times and responsiveness issues, depending on the size of your genome files. This program is best executed on local workstations rather than a shared server. || | ||
+ | |- | ||
+ | | [https://pypi.org/project/iced/ iced] || v0.5.1 || Done || - || | ||
+ | |- | ||
+ | | [http://www.novocraft.com/products/novoalign/ novoalign] || v3.03.01 || Done || - || | ||
+ | |- | ||
+ | | [https://cutadapt.readthedocs.io/en/stable/guide.html#basic-usage cutadapt] || v1.12 and v. 3.3 || Done || The default and EOLed Python 2.7 environment has version 1.12 accessible by the shell. To access the more up-to-date and parallel/multi-core capable version of 3.3, you need to enable the python 3.8 environment in your shell by typing: | ||
+ | scl enable rh-python38 bash | ||
+ | | | ||
+ | |- | ||
+ | | [https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml FASTA] || v36.3.8b Oct, 2015 || Done || - || | ||
+ | |- | ||
+ | | [https://github.com/nservant/HiC-Pro HiC-Pro] || v2.11.0-beta || Done || Compiled for python 2.7.5 against bx-python 0.8.2, numpy 1.14.2, scipy 1.0.1 || | ||
+ | |- | ||
+ | | [https://ccb.jhu.edu/software/hisat2/index.shtml Hisat] || v2.1.0 || Done || Compiled locally with gcc version 7.3.1-5 || | ||
+ | |- | ||
+ | | iMir || - || Done || Type <code>launch_iMir</code> to start the GUI || | ||
+ | |- | ||
+ | | [https://intervene.readthedocs.io/en/latest/introduction.html Intervene] || v0.6.5 || Done || <code>scl enable rh-python38 bash</code> || | ||
|- | |- | ||
− | | | + | | [https://github.com/tare/Lux Lux] || latest commit 15/03/2016 || Done || Based on STAR version 2.11.0 which is also installed on the server. || |
|- | |- | ||
− | | | + | | [http://liulab.dfci.harvard.edu/MACS/00README.html macs14] || v1.4.2 20120305 || Done || - || |
|- | |- | ||
− | | | + | | [https://github.com/taoliu/MACS macs2] || v2.1.0.20150731 || Done || - || |
|- | |- | ||
− | | | + | | [http://smithlabresearch.org/software/methpipe/ MethPipe] || v3.4.2 || Done || - || |
|- | |- | ||
− | | | + | | [http://smithlabresearch.org/software/methpipe/ Methy-Pipe] || v2.1 || Done || - || |
|- | |- | ||
− | | | + | | [https://github.com/milaboratory/mixcr mixcr] || v2.1.5 || Done || - || |
|- | |- | ||
− | | | + | | [https://github.com/shenlab-sinai/ngsplot ngs.plot] || v2.61 || Done || - || |
|- | |- | ||
− | | | + | | [https://github.com/wassermanlab/oPOSSUM3 oPOSSUM3] || Latest git commit 01/2016 || Done || RDBMS that holds the JASPER and other TFBS databases on hfaistos.uio.no. Biotin2.hpc only has the client programs. See [https://rt.uio.no/Ticket/Display.html?id=235025 UiO RT 235025]. || |
|- | |- | ||
− | | | + | |[https://www.gnu.org/software/octave/ GNU Octave] |
+ | |v4.4.1 | ||
+ | |Done | ||
+ | |Dependencies on HDF5 and SuiteSparse. Built from source. | ||
+ | | | ||
|- | |- | ||
− | | | + | | [http://smithlabresearch.org/software/preseq/ preseq] || v2.0.1 || Done || Tarball from source reports version 2.0.1, yet the tool reports version 2.0.0. Version error from the authors. || |
|- | |- | ||
− | | | + | |[https://github.com/EGA-archive/ega-download-client pyega3] |
+ | |pyEGA3 - EGA python client version 3.0.44 | ||
+ | |Done | ||
+ | |To use the pyega3, you need to load the Python 36 client by typing first: | ||
+ | '''scl enable rh-python36 bash''' | ||
+ | | | ||
|- | |- | ||
− | | | + | | [http://pedagogix-tagc.univ-mrs.fr/rsat/RSAT_portal.html RSAT] || opting for the latest github version as dictated by the NCMM Computational Biology Group || Done || Command line version RSAT tools reference their own versions of NCBI BLAST and [http://www.vmatch.de/ vmatch] tools || |
|- | |- | ||
− | | | + | | [https://ccb.jhu.edu/software/stringtie/index.shtml StringTie] || v1.3.4d || Done || Compiled locally with gcc version 7.3.1-5 || |
|- | |- | ||
− | | | + | |[http://subread.sourceforge.net/ subread] |
+ | |v1.6.3 | ||
+ | |Done | ||
+ | |Associated to this is the [https://bioconductor.org/packages/release/bioc/html/Rsubread.html Rsubread Bioconductor package]. | ||
+ | | | ||
|- | |- | ||
− | | | + | | [https://www.ebi.ac.uk/~zerbino/velvet/ velvet] || v1.2.10 || Done || - || |
|- | |- | ||
− | | | + | | [http://www.vmatch.de/ vmatch] || v2.3.0 || Done || Usually required for the RSAT tool, but offered as a standalone utility outside the RSAT program PATH. || |
|- | |- | ||
− | | | + | | [https://github.com/xie186/ViewBS ViewBS] || git repo date 2/11/2018 || Done || - || |
|- | |- | ||
− | | | + | | [https://github.com/ncbi/sra-tools/wiki/Downloads NCBI SRA Toolkit (sra-tools)] || v2.5.4.1 || Done || - || |
|- | |- | ||
− | | | + | | [https://bedtools.readthedocs.io/en/latest/index.html bedtools] || v2.30.0 || Done || to use, please run, e.g., <code>module load bedtools/2.30.0</code> || |
|- | |- | ||
− | | | + | | [http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml ChIPseeqer] || v2.0 || Done || Observed many compiler warnings during the build. Users should clarify whether version 2.1 should be installed. The software looks old and unmaintained. || |
|- | |- | ||
− | | | + | | [http://xds.mpimf-heidelberg.mpg.de/ XDS] || BUILT=20180319 || Done || KMP_STACKSIZE=8m is exported by default on the shell. If you need to increase that, please raise an RT ticket || |
|- | |- | ||
− | | | + | | [http://www.phenix-online.org/documentation/index.html PHENIX] || v1.19rc7-4070 || Done || - || |
|- | |- | ||
− | | | + | | [http://www.ccp4.ac.uk/index.php CCP4] || v7.1.003 || Done || Users need to manually do: <code>source /lsc/ccp4/7.1.003/bin/ccp4.setup-sh</code> prior using the package due to numpy conflicts with other applications. || |
|- | |- | ||
− | | | + | | [http://broadinstitute.github.io/picard/ picard] || v1.140 || Done || Based on HTSJDK v1.140 || |
|- | |- | ||
− | | | + | | [http://circos.ca/ circos] || v0.68 || Done || - || |
|- | |- | ||
− | | | + | | [https://software.broadinstitute.org/gatk/ The Genome Analysis ToolKit (GATK)] || v3.4-46-gbc02625 || Done || - || |
|- | |- | ||
− | | | + | | [https://htseq.readthedocs.io/en/release_0.11.1/ HTSeq] || v0.6.1 || Done || - || |
|- | |- | ||
− | | | + | | [https://github.com/ComputationalRegulatoryGenomicsICL/TFBS/ Perl TFBS] || v0.7.0 || Done || The Perl TFBS module is installed but is not in active development. Instead, we have installed the TFBStools (R/Bioconductor). || |
|- | |- | ||
− | | | + | | [http://smithlabresearch.org/software/preseq/ preseq] || v2.0.1 || Done || - || |
|- | |- | ||
− | | | + | | [https://pythonhosted.org/pyDNase/index.html pyDNase] || github repo clone 30/05/2017 || Done || - || |
|- | |- | ||
− | | | + | | [https://deweylab.github.io/RSEM/ RSEM] || v1.3.0 || Done || - || |
|- | |- | ||
− | | | + | | [https://code.google.com/archive/p/rna-star/ STAR] || v2.5.3a || Done || - || |
|- | |- | ||
− | | | + | | [http://liulab.dfci.harvard.edu/CEAS/ CEAS] || v1.0.2 || Done || - || |
|- | |- | ||
− | | | + | | [http://qualimap.bioinfo.cipf.es/ Qualimap] || v2.2.1 || Done || linked to the Sun JAVA JRE (/lsc/sources/jre1.7.0_80/bin/java). All R dependencies installed. || |
|- | |- | ||
− | | | + | | [http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html Quest] || v.2.4 || Done || - || |
|- | |- | ||
− | | | + | | [https://home.gwu.edu/~wpeng/Software.htm SICER] || v1.1 || Done || - || |
|- | |- | ||
− | | | + | |velocyto |
+ | |0.17.17 | ||
+ | |Done | ||
+ | |Compiled against Python 3.6.9, so to initialize it properly do: | ||
+ | '''scl enable rh-python36 bash''' | ||
+ | |||
+ | To initialize the R module properly, do: | ||
+ | |||
+ | '''scl enable rh-python36 bash''' | ||
+ | |||
+ | '''module load R/3.6.1''' | ||
+ | | | ||
|- | |- | ||
− | | | + | | [https://github.com/dmlc/xgboost XGBoost] || Latest github commit on 06/04/2017 || Done || Installed Python 2.7.x module, command line compiled utility and R module. || |
|- | |- | ||
− | | | + | | [https://github.com/LiuLabUB/HMMRATAC HMMRATAC] || v1.2.9 || Done || module load hmmratac/1.2.9; hmmratac (aliased to "/usr/bin/java -jar /$lsc/$package/$version/$package") || |
|- | |- | ||
− | | | + | | [https://github.com/jsh58/Genrich Genrich] || v0.6 || Done || module load genrich/0.6; genrich || |
|- | |- | ||
− | | | + | | [https://github.com/Dowell-Lab/DAStk DAStk] || Latest github commit on 2020--01-14 || Done || scl enable rh-python36 || |
|- | |- | ||
− | | | + | | [https://github.com/ewels/MultiQC MultiQC] || 0.2.3 || Done || on biotin2: scl enable rh-python36; conda activate /lsc/multiqc/1.8 on biotin3: scl enable rh-python36; source activate /lsc/multiqc/1.8 (older version of conda) || |
|- | |- | ||
− | | | + | | [http://cbio.mskcc.org/miRNA2003/miranda.html miRanda] || v1.9 || Done || <code>'''module load miRanda/1.9'''</code> || |
|- | |- | ||
− | | | + | |[https://github.com/usadellab/Trimmomatic trimmomatic] |
+ | |v0.4.0 | ||
+ | |Done | ||
+ | |To execute, use the JRE by typing: | ||
+ | <code>'''java -jar /lsc/trimmomatic/trimmomatic-0.40-rc1.jar'''</code> | ||
+ | | | ||
|- | |- | ||
− | | | + | |[https://github.com/LiuzLab/SalmonTE SalmonTE] |
+ | |v0.4 | ||
+ | |Done | ||
+ | |Installed with the Python 3.8 and R 4.0.2 applications, so to access it type: | ||
+ | <code>'''scl enable rh-python38 bash'''</code> | ||
+ | |||
+ | <code>'''module load R/4.0.2'''</code> | ||
+ | | | ||
|- | |- | ||
− | | | + | |[https://github.com/FelixKrueger/TrimGalore trim_galore] |
+ | |v0.6.6 | ||
+ | |Done | ||
+ | | - | ||
+ | | | ||
|- | |- | ||
|} | |} | ||
+ | |||
+ | == Top Directory ( /lsc ) == | ||
+ | |||
+ | The top directory for all installed software is <code>/lsc</code> | ||
+ | |||
+ | == How applications are run on biotin2 and biotin3 == | ||
+ | |||
+ | === R 3.6.1 === | ||
+ | |||
+ | R 3.6.1 is run as a module. | ||
+ | |||
+ | In order to use 3.6.1 type | ||
+ | |||
+ | module load R/3.6.1 | ||
+ | |||
+ | |||
+ | ==== R 3.6.1, /usr/bin/screen and RedHat Software Collections (/usr/bin/scl) ==== | ||
+ | |||
+ | |||
+ | Be careful when using the RedHat Software Collections: /usr/bin/scl resets your user environment, because it re-reads your .login/.bash_login/.profile/.bash_profile when it starts up (as it executes as a login shell) | ||
+ | |||
+ | /usr/bin/screen does the same thing: it re-reads your .login/.bash_login/.profile/.bash_profile and, therefore it resets your environment. | ||
+ | |||
+ | |||
+ | |||
+ | Should you want to use modules, screen, and the RedHat Software collection, the correct order is to: | ||
+ | |||
+ | # login in bioin2 or biotin3 | ||
+ | # run /usr/bin/screen | ||
+ | # then scl rh-example8 enable bash | ||
+ | # finally, module load R/3.6.1 |
Latest revision as of 10:06, 4 May 2023
biotin2
is a departmental general use server for the "in silico" groups.
biotin3
is the Mathelier group server for its exclusive use.
Contents
Description of the biotin[2,3].hpc.uio.no servers and associated VMs with replicated applications
- biotin2: 128 Intel Haswell cores, 1 Tb RAM, 162 Tb of local disk space allocated for various NCMM groups
- biotin3: 192 Intel Broadwell cores, 1 Tb RAM, 5 Tb of local disk space allocated as scratch and local partitions for the Mathelier Group.
- kuijjer2: 24 AMD EPYC virtual cores, 128 Gb RAM, 5 Tb of local disk space for the Kuijjer Group
- waszak1: 48 AMD EPYC virtual cores, 128 Gb RAM, 4 Tb of local disk space for the Waszak Group
List of software installed on the biotin[2,3].hpc.uio.no servers and VMs
Application | Version on biotin2.hpc.uio.no and biotin3.hpc.uio.no | Status | Comments | |
MATLAB | R2019b (9.7.0.1216025) 64-bit (glnxa64) | Done | University of Oslo Site License | |
R with Bioconductor | R version 3.5.1 (2018-07-02) "Feather Spray" (3.5.1 is not in active maintenance ) R version 3.6.1 (2019-07-05) "Action of the Toes" R version 4.0.2 (2020-04-02) "Taking Off Again" |
Done | To access R v. 3.6.1, type:
- To access R v. 4.0.2, type: - |
|
Perl | v5.16.3 | Done | Upgraded version should not cause any problems | |
Perl 6 | 6c | Done | Based on Rakudo Star release 17.4 | |
Python | Python 2.7.5, as well as 3,4,2, 3.5.1, 3.6.9 and 3.8.0 from RedHat Software Collections plus installed scientific computing modules. For a list of Python modules we maintain, please visit this page. | Done | To access the default Python 2.7 environment, you need to type nothing.
Please note the End Of Life (EOL) of Python 2.7.x . Make an effort to use Python 3.x instead, as described below. To enable the Python 3 version, please type on your shell -For version 3.4.2:
-For version 3.5.1:
-For version 3.6.9:
-For version 3.8.0:
|
|
ataqv | 1.0.0 | Done | ataqv was built against the HTSLIB in /lsc/htslib and with gcc 8.2.1 (devtoolset-8) | |
bamliquidator | Latest commit c2c4865, Oct 3, 2017 | Done | Compiled against HDF5 lib version 1.8.22 | |
BGSignature | 0.2 | Done | Installed with Python 3.6, so to use it, do a:
scl enable rh-python36 bash |
|
BiasAway | norpy version | Done | - | |
Bismark | v0.16.3_dev | Done | - | |
bowtie | version 1.1.2 64-bit | Done | Old bowtie genomic indices were transferred from biotin in /lsc/bowtie1ind | |
bowtie2 | version 2.3.4.1 64-bit | Done | Old bowtie2 genomic indices were transferred from biotin in /lsc/bowtie2ind | |
bedops | version 2.4.14 | Done | - | |
bsExpress | v0.5cegx | Done | The sofware was modified/fixed to run properly on our production environment. Patches are described in UiO RT case #2444978. | |
bsmap | version 2.74 | Done | - | |
bwa | Version: 0.7.12-r1039 | Done | - | |
bwa-meth | Version 0.2.0 | Done | - | |
blast (NCBI) | 2.2.30+ | Done | Blast DBs were transferred from biotin in /lsc/blastdbs |
|
cta | 0.1.2 | Done | Compiled with gcc 8.2.1 (devtoolset-8). It does not compile gcc 4.x . | |
chimera | 1.15 | Done | - . | |
datamash | 1.1.1 | Done | - | |
eman | 2.31 | Done | source /lsc/eman/2.31/etc/profile.d/conda.sh WARNING: PYTHONPATH set, might interfere with eman2 | |
DNAshapedTFBS | Latest commit 418fff6 on 28 Sep 2016 | Done | - | |
samtools | 1.3.1 | Done | Samtools is used by certain applications as a dependency. Some of these applications might require older versions of the samtools. These cases will be dealt on a "as needed" basis. | |
tophat and tophat2 | v2.1.0 | Done | - | |
FastQ Screen | v0.5.2 | Done | - | |
fastQC | v0.11.4 | Done | - | |
gcc 6 compiler | v6.3.1 | Done | Default compiler for RHEL 7 is gcc 4.8.x. We include as well gcc version 6. To use type at your shell prompt: scl enable devtoolset-6 bash |
|
gcc 7 compiler | v7.3.1 | Done | Default compiler for RHEL 7 is gcc 4.8.x. We include as well gcc version 7. To use type at your shell prompt: scl enable devtoolset-7 bash |
|
gcc 8 compiler | v8.2.1 | Done | To use type at your shell prompt: scl enable devtoolset-8 bash
|
|
Expression analysis ea-utils | github repo 31/10/2017 | Done | - | |
edd | v1.1.14 | Done | This is a new installation of the latest Enriched Domain Detector (EDD) software based on the system wide installed Python 2.7.5 and the following dependency component versions Cython-0.23.4 numpy-1.10.1 pysam-0.8.3 scipy-0.16.1 pandas-0.17.0 patsy-0.4.0 and statsmodels-0.6.1. Biotin used to run this for specific users using manually compiled Python 2.7.9. Recommended to re-run some data to check if the same results are achieved prior using the software, as a precaution. | |
EMBOSS | v6.6.0.0 | Done | - | |
BroadPeak | - | Done | Depended on R and Perl versions. Working. | |
cufflinks | v2.2.1 | Done | Installed against the RHEL7 dependency libraries boost version 1.53, eigen3-devel version 3.2.5, boost-bjam | |
Homer Tools | v4.7.2 | Done | Configurable by the end users, installed genomes hg(17-19),mm(8-10),xenTro(2,3),ce(6,10),danRer7, galGal4,rn5 | |
meme | v.4.11.4 | Done | No sequence databases were downloaded on biotin, hence no databases on biotin2 | |
ViennaRNA | v2.1.9 | Done | - | |
F-Seq | v1.8.4 | Done | In biotin2 we have JAVAOPTS="-Xmx16000M" as opposed to JAVAOPTS="-Xmx8000M" of biotin (twice the heap size) configued in fseq | |
WEKA | v3.7.13 | Done | Type launch_weka to start the GUI of the program. Check the functionality against Java 1.8 . Heap size is set to 4 Gig. (4 x biotin size) |
|
IGV | v2.3.88 | Done | Type igv.sh to start the browser. Expect long startup times and responsiveness issues, depending on the size of your genome files. This program is best executed on local workstations rather than a shared server. |
|
iced | v0.5.1 | Done | - | |
novoalign | v3.03.01 | Done | - | |
cutadapt | v1.12 and v. 3.3 | Done | The default and EOLed Python 2.7 environment has version 1.12 accessible by the shell. To access the more up-to-date and parallel/multi-core capable version of 3.3, you need to enable the python 3.8 environment in your shell by typing:
scl enable rh-python38 bash |
|
FASTA | v36.3.8b Oct, 2015 | Done | - | |
HiC-Pro | v2.11.0-beta | Done | Compiled for python 2.7.5 against bx-python 0.8.2, numpy 1.14.2, scipy 1.0.1 | |
Hisat | v2.1.0 | Done | Compiled locally with gcc version 7.3.1-5 | |
iMir | - | Done | Type launch_iMir to start the GUI |
|
Intervene | v0.6.5 | Done | scl enable rh-python38 bash |
|
Lux | latest commit 15/03/2016 | Done | Based on STAR version 2.11.0 which is also installed on the server. | |
macs14 | v1.4.2 20120305 | Done | - | |
macs2 | v2.1.0.20150731 | Done | - | |
MethPipe | v3.4.2 | Done | - | |
Methy-Pipe | v2.1 | Done | - | |
mixcr | v2.1.5 | Done | - | |
ngs.plot | v2.61 | Done | - | |
oPOSSUM3 | Latest git commit 01/2016 | Done | RDBMS that holds the JASPER and other TFBS databases on hfaistos.uio.no. Biotin2.hpc only has the client programs. See UiO RT 235025. | |
GNU Octave | v4.4.1 | Done | Dependencies on HDF5 and SuiteSparse. Built from source. | |
preseq | v2.0.1 | Done | Tarball from source reports version 2.0.1, yet the tool reports version 2.0.0. Version error from the authors. | |
pyega3 | pyEGA3 - EGA python client version 3.0.44 | Done | To use the pyega3, you need to load the Python 36 client by typing first:
scl enable rh-python36 bash |
|
RSAT | opting for the latest github version as dictated by the NCMM Computational Biology Group | Done | Command line version RSAT tools reference their own versions of NCBI BLAST and vmatch tools | |
StringTie | v1.3.4d | Done | Compiled locally with gcc version 7.3.1-5 | |
subread | v1.6.3 | Done | Associated to this is the Rsubread Bioconductor package. | |
velvet | v1.2.10 | Done | - | |
vmatch | v2.3.0 | Done | Usually required for the RSAT tool, but offered as a standalone utility outside the RSAT program PATH. | |
ViewBS | git repo date 2/11/2018 | Done | - | |
NCBI SRA Toolkit (sra-tools) | v2.5.4.1 | Done | - | |
bedtools | v2.30.0 | Done | to use, please run, e.g., module load bedtools/2.30.0 |
|
ChIPseeqer | v2.0 | Done | Observed many compiler warnings during the build. Users should clarify whether version 2.1 should be installed. The software looks old and unmaintained. | |
XDS | BUILT=20180319 | Done | KMP_STACKSIZE=8m is exported by default on the shell. If you need to increase that, please raise an RT ticket | |
PHENIX | v1.19rc7-4070 | Done | - | |
CCP4 | v7.1.003 | Done | Users need to manually do: source /lsc/ccp4/7.1.003/bin/ccp4.setup-sh prior using the package due to numpy conflicts with other applications. |
|
picard | v1.140 | Done | Based on HTSJDK v1.140 | |
circos | v0.68 | Done | - | |
The Genome Analysis ToolKit (GATK) | v3.4-46-gbc02625 | Done | - | |
HTSeq | v0.6.1 | Done | - | |
Perl TFBS | v0.7.0 | Done | The Perl TFBS module is installed but is not in active development. Instead, we have installed the TFBStools (R/Bioconductor). | |
preseq | v2.0.1 | Done | - | |
pyDNase | github repo clone 30/05/2017 | Done | - | |
RSEM | v1.3.0 | Done | - | |
STAR | v2.5.3a | Done | - | |
CEAS | v1.0.2 | Done | - | |
Qualimap | v2.2.1 | Done | linked to the Sun JAVA JRE (/lsc/sources/jre1.7.0_80/bin/java). All R dependencies installed. | |
Quest | v.2.4 | Done | - | |
SICER | v1.1 | Done | - | |
velocyto | 0.17.17 | Done | Compiled against Python 3.6.9, so to initialize it properly do:
scl enable rh-python36 bash To initialize the R module properly, do: scl enable rh-python36 bash module load R/3.6.1 |
|
XGBoost | Latest github commit on 06/04/2017 | Done | Installed Python 2.7.x module, command line compiled utility and R module. | |
HMMRATAC | v1.2.9 | Done | module load hmmratac/1.2.9; hmmratac (aliased to "/usr/bin/java -jar /$lsc/$package/$version/$package") | |
Genrich | v0.6 | Done | module load genrich/0.6; genrich | |
DAStk | Latest github commit on 2020--01-14 | Done | scl enable rh-python36 | |
MultiQC | 0.2.3 | Done | on biotin2: scl enable rh-python36; conda activate /lsc/multiqc/1.8 on biotin3: scl enable rh-python36; source activate /lsc/multiqc/1.8 (older version of conda) | |
miRanda | v1.9 | Done | module load miRanda/1.9 |
|
trimmomatic | v0.4.0 | Done | To execute, use the JRE by typing:
|
|
SalmonTE | v0.4 | Done | Installed with the Python 3.8 and R 4.0.2 applications, so to access it type:
|
|
trim_galore | v0.6.6 | Done | - |
Top Directory ( /lsc )
The top directory for all installed software is /lsc
How applications are run on biotin2 and biotin3
R 3.6.1
R 3.6.1 is run as a module.
In order to use 3.6.1 type
module load R/3.6.1
R 3.6.1, /usr/bin/screen and RedHat Software Collections (/usr/bin/scl)
Be careful when using the RedHat Software Collections: /usr/bin/scl resets your user environment, because it re-reads your .login/.bash_login/.profile/.bash_profile when it starts up (as it executes as a login shell)
/usr/bin/screen does the same thing: it re-reads your .login/.bash_login/.profile/.bash_profile and, therefore it resets your environment.
Should you want to use modules, screen, and the RedHat Software collection, the correct order is to:
- login in bioin2 or biotin3
- run /usr/bin/screen
- then scl rh-example8 enable bash
- finally, module load R/3.6.1