Difference between revisions of "Biotin2.hpc.uio.no"

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(Software Installed, List of)
Line 26: Line 26:
| [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
|Compiled against HDF5 lib version 1.8.22
| [https://github.com/wassermanlab/BiasAway BiasAway]                                || norpy version                                                                                  || Done  || - ||
| [https://github.com/wassermanlab/BiasAway BiasAway]                                || norpy version                                                                                  || Done  || - ||

Revision as of 15:04, 31 January 2019

biotin2 is the departamental general usage server for the 'in silico' groups.

biotin3 is the Mathelier group server for their exclusive use.

Description of the biotin[2,3].hpc.uio.no servers

  • 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.

List of software installed on the biotin[2,3].hpc.uio.no servers

Application Version on biotin2.hpc.uio.no and biotin3.hpc.uio.no Status Comments
MATLAB R2018b ( 64-bit (glnxa64) Done Currently testing the University site license 2018b version. Seems to be stable. Previous production version 2017a
R with Bioconductor R version 3.5.1 (2018-07-02) -- "Feather Spray" Done latest bioconductor modules are applied according to version tool dependencies.
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 (default, Apr  9 2015, 11:03:32) and Python 3.5.1 from RedHat Software collections Done  In a similar way to R, certain Python modules (pip install) might need re-installation. This will be considered again on a "as needed" basis for specific critical applications. To enable the Python 3 version, please type on your shell: scl enable rh-python35 bash
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
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 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 .
datamash Version 1.1.1 Done -
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 Done One of the many dependencies for iMir
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 v0.5.6 git commit 22/02/2017 Done -
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 - [broken] 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.
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.
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
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 -
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 v1.10.1-2155 Done -
CCP4 v6.5 Done Users need to manually do: source /lsc/ccp4/ccp4-6.5/bin/ccp4.setup-sh prior using the package due to numpy conflicts with other applications.
bedtools v2.25.0 Done -
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 -
XGBoost Latest github commit on 06/04/2017 Done Installed Python 2.7.x module, command line compiled utility and R module.

Top Directory ( /lsc )

Top directory for all installed software is /lsc

How are applications are run on biotin2/3