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Software installation list update #7

Open muslih14 opened 7 years ago

muslih14 commented 7 years ago

Of the fourteen software, I requested ITS to install five are yet to be installed. These are :

  1. LMAT (Livermore Metagenomics Analysis Toolkit): http://computation.llnl.gov/projects/lmat-livermore-metagenomics-analysis-toolkit/software

  2. HUMAnN:https://huttenhower.sph.harvard.edu/humann

  3. Bracken(Bayesian Reestimation of Abundance with KrakEN):https://ccb.jhu.edu/software/bracken/

  4. DuDes:https://sourceforge.net/projects/dudes/

  5. CLARK:http://clark.cs.ucr.edu/

  6. GOTTCHA:https://github.com/poeli/GOTTCHA

I'm also looking to install the following in addition, probably by myself in the next few weeks:

CENTRIFUGE : https://ccb.jhu.edu/software/centrifuge/index.shtml METASHOT: https://github.com/bfosso/MetaShot KRAKEN:https://ccb.jhu.edu/software/kraken/

grahamgower commented 7 years ago

LMAT is installed. You'll need to export MODULEPATH=/data/acad/apps/modules/all:$MODULEPATH first in order to access this, as per the Modules page on the wiki.

HUMAnN has no installation procedure per se, simply uncompress the .tar.gz file and follow the instructions in the README.text. It does depend on some other software, e.g. scons. You can identify the correct module to load using e.g. module spider scons.

I'll try to take a look at the other stuff this week.

muslih14 commented 7 years ago

Casava - a software tool to convert bcl2fastq is missing from the cluster.
https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html

yassineS commented 7 years ago

bcl2fastq is a real pain in the ass to compile. I had several back-and-forth emails with ITS, and they didn't manage to compile it. @grahamgower There are Fedora binaries available, is there any chance we can make those work some way? I'm not sure what's the underlying architecture on the hosts? Always assumed it's scientific linux, in which case the rpm will do the trick.

grahamgower commented 7 years ago

Yes, we can probably make Fedora binaries work somehow. Ping me next week and I'll continue working on this ticket!

grahamgower commented 7 years ago

The steaming pile that is bcl2fastq is now installed as module bcl2fastq/2.19.1.403. Note there's also a version bcl2fastq/2.17.1.14-foss-2106a - don't use this, as it won't play nice with any other modules you have loaded.

yassineS commented 7 years ago

You’re a gem Graham.

Thanks, —Yassine

On 25 Aug 2017, 10:29 AM +0930, Graham Gower notifications@github.com, wrote:

The steaming pile that is bcl2fastq is now installed as module bcl2fastq/2.19.1.403. Note there's also a version bcl2fastq/2.17.1.14-foss-2106a - don't use this, as it won't play nice with any other modules you have loaded. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

muslih14 commented 7 years ago

Thanks, Graham!

On Fri, Aug 25, 2017 at 7:54 PM, Yassine Souilmi notifications@github.com wrote:

You’re a gem Graham.

Thanks, —Yassine

On 25 Aug 2017, 10:29 AM +0930, Graham Gower notifications@github.com, wrote:

The steaming pile that is bcl2fastq is now installed as module bcl2fastq/2.19.1.403. Note there's also a version bcl2fastq/2.17.1.14-foss-2106a - don't use this, as it won't play nice with any other modules you have loaded. — You are receiving this because you commented.

Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ACAD-UofA/Bioinformatics-Wiki/issues/7#issuecomment-324880475, or mute the thread https://github.com/notifications/unsubscribe-auth/APRho8q6ScuFhw_KMXSaek6Hl_n_Mckiks5sbqDKgaJpZM4OTlud .

-- Best wishes,

Muslihudeen (Muslih) Abdul-Aziz http://www.adelaide.edu.au/directory/muslihudeen.abdul-aziz

PhD candidate Australian Centre for Ancient DNA http://www.adelaide.edu.au/acad/ (ACAD), School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005 Australia. Ph: +61 (0) 88313 8245

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I acknowledge the Kaurna peoples, the traditional custodians of the Adelaide region past, present and forever more, on whose land the Australian Centre for Ancient DNA is built. I wish to pay respect to Elders both past and present.