Difference between revisions of "Biotin2.hpc.uio.no"
(Updated Python 3.x versions and inserted info about the velocyto application.) (Tag: Visual edit) |
(→List of software installed on the biotin[2,3].hpc.uio.no servers) |
||
Line 238: | Line 238: | ||
|- | |- | ||
| [https://github.com/Dowell-Lab/DAStk DAStk] || Latest github commit on 2020--01-14 || Done || scl enable rh-python36 || | | [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) || | ||
|- | |- | ||
|} | |} |
Revision as of 11:09, 30 April 2020
biotin2
is the departamental general usage server for the 'in silico' groups.
biotin3
is the Mathelier group server for their exclusive use.
Contents
Live computational resource usage information (cpu and memory) - Biotin2
Live computational resource usage information (cpu and memory) - Biotin3
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 (9.5.0.944444) 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 and other R 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, 3.5.1 and 3.6.9 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 3.5.1:
-For version 3.6.9:
|
|
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 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 . | |
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 | 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. | |
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 | - | |
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 | - | |
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) |
Top Directory ( /lsc )
Top directory for all installed software is /lsc
How are applications are run on biotin2/3
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 bioin2/3
- run /usr/bin/screen
- then scl rh-example8 enable bash
- finally, module load R/3.6.1