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6 years, 326 days, 23 hours and 53 minutes - Benoit Charloteaux

Difference between revisions of "Main Page"
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===[[Grid_computing|Grid]]-based tools===
 
===[[Grid_computing|Grid]]-based tools===
−
<console>
+
<center>
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u227664@master01:~$ ##i##module avail
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{| class="wikitable"
−
 
+
|-
−
##b##----------------------------------------------------------------------- /cm/shared/modulefiles ------------------------------------------------------------------------
+
| 5.3.1 || bowtie/2.3.3.1 || elprep/2.61 || gnuplot/5.0.6 || lapack/gcc/64/3.5.0 || perl/time-piece/1.31 || scala/2.12.0
−
5.3.1                     bowtie/2.3.3.1           elprep/2.61               gnuplot/5.0.6             lapack/gcc/64/3.5.0       perl/time-piece/1.31     scala/2.12.0
+
|-
−
bam-readcount/1           bwa/0.7.15               elprep/3.0               go/1.9                   mothur/1.39.1             picard-tools/1.78         seqff/1
+
| bam-readcount/1 || bwa/0.7.15 || elprep/3.0 || go/1.9 || mothur/1.39.1 || picard-tools/1.78 || seqff/1
−
basespace-invaders/1.0.0 bwa/0.7.16a               elprep/3.01               hdf5/1.6.10               nanonet/1                 picard-tools/2.7.1       singularity/2.2.1
+
|-
−
basespace-python/1.0.0   bwa/0.7.5a               emboss/6.6.0             hdf5_18/1.8.14           ncbi/eutils/2016-11-22   puppet/3.7.5             slurm/14.11.11
+
| basespace-invaders/1.0.0 || bwa/0.7.16a || elprep/3.01 || hdf5/1.6.10 || nanonet/1 || picard-tools/2.7.1 || singularity/2.2.1
−
bcftools/1.3.1           canu/1.4                 ensembl-tools/86         homer/4.9                 netperf/2.6.0             R/3.2.2                   snpeff/4
+
|-
−
bcl2fastq/2.17           cellranger/1.3.1         excelcompare/0.6.1       hpl/2.1                   openblas/dynamic/0.2.14   R/3.2.4                   star/2.5.2b
+
| basespace-python/1.0.0 || bwa/0.7.5a || emboss/6.6.0 || hdf5_18/1.8.14 || ncbi/eutils/2016-11-22 || puppet/3.7.5 || slurm/14.11.11
−
beagle/21jan17           cmgui/7.1                 fastqc/0.11.5             htseq/0.6.1p1             openlava/3.0             rdp-classifier/2.6       sun-jre/7
+
|-
−
beagle/3.3.2             crispresso/1             fastx_toolkit/0.0.13     htslib/1.3.2             openmpi/gcc/64/1.8.5     rdptools/1               tabix/0.2.6
+
| bcftools/1.3.1 || canu/1.4 || ensembl-tools/86 || homer/4.9 || netperf/2.6.0 || R/3.2.2 || snpeff/4
−
bedtools/2.17.0           cufflinks/2.2.1           flash/1.2.11             igvtools/2.3.78           pandoc/1.16.0.2           rmats/3.2.5               tophat/2.1.1
+
|-
−
blas/gcc/64/3.5.0         cutadapt/1.11             gatk/3.1.1               iozone/3_430             penncnv/1.0.3             sambamba/0.6.6           ucsc/utils/v432
+
| bcl2fastq/2.17 || cellranger/1.3.1 || excelcompare/0.6.1 || hpl/2.1 || openblas/dynamic/0.2.14 || R/3.2.4 || star/2.5.2b
−
blast/2.5.0+             default-environment       gatk/3.6                 iozone/3_471             perl/5.16.3               samstat/1.5.1             vcfsorter/1
+
|-
−
blat/35                   dos2unix/7.1             gdb/7.9                   java/7.0.25               perl/5.24.1               samtools/0.1.19           vcftools/1
+
| beagle/21jan17 || cmgui/7.1 || fastqc/0.11.5 || htseq/0.6.1p1 || openlava/3.0 || rdp-classifier/2.6 || sun-jre/7
−
bonnie++/1.97.1           EasyBuild                 genomicsimla/1.1.3       java/8.0.111             perl/config-simple/4.59   samtools/1.3.1           vep/90
+
|-
−
bowtie/1.1.2             ea-utils/27               GNUparallel/20160822     jdk/jdk1.8.0_66           perl/test-simple/1,001014 samtools/1.6             zlib/1.2.8
+
| beagle/3.3.2 || crispresso/1 || fastx_toolkit/0.0.13 || htslib/1.3.2 || openmpi/gcc/64/1.8.5 || rdptools/1 || tabix/0.2.6
−
</console>
+
|-
 +
| bedtools/2.17.0 || cufflinks/2.2.1 || flash/1.2.11 || igvtools/2.3.78 || pandoc/1.16.0.2 || rmats/3.2.5 || tophat/2.1.1
 +
|-
 +
| blas/gcc/64/3.5.0 || cutadapt/1.11 || gatk/3.1.1 || iozone/3_430 || penncnv/1.0.3 || sambamba/0.6.6 || ucsc/utils/v432
 +
|-
 +
| blast/2.5.0+ || default-environment || gatk/3.6 || iozone/3_471 || perl/5.16.3 || samstat/1.5.1 || vcfsorter/1
 +
|-
 +
| blat/35 || dos2unix/7.1 || gdb/7.9 || java/7.0.25 || perl/5.24.1 || samtools/0.1.19 || vcftools/1
 +
|-
 +
| bonnie++/1.97.1 || EasyBuild || genomicsimla/1.1.3 || java/8.0.111 || perl/config-simple/4.59 || samtools/1.3.1 || vep/90
 +
|-
 +
| bowtie/1.1.2 || ea-utils/27 || GNUparallel/20160822 || jdk/jdk1.8.0_66 || perl/test-simple/1,001014 || samtools/1.6 || zlib/1.2.8
 +
|}
 +
</center>
  
  

Revision as of 13:23, 12 November 2017

For further informations, please contact :

GIGA UDI Med
GIGA +1, Room 1/11A-B

laurent.fournier@uliege.be
Work: +32 4 366 34 53
Mobile: +32 497 87 96 46

CHU +0

udi.med@uliege.be
+32 4 366 99 66
Requests form

  • Linux support & management
  • MassStorage + grids's support & management
  • Taping system (backup)
  • Support & installs grid Linux-based
  • Desk Support & management
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  • Support & installs office Windows/Mac-based
And, of course, you still got the ULg Intranet for all administrative requests and the GIGA Intranet providing much more informations.



What we got right now

Web-based tools

This Wiki - Information board About
OpenAtrium - A Project Manager for Usergroups, tasks and logistics management About Howto
Galaxy - A bioinformatics research platform About Howto
Cytomine - A collaborative imaging analysis platform About Howto
RStudio - A web IDE for R About Howto
GitLab - A versioning platform About Howto


Grid-based tools

5.3.1 bowtie/2.3.3.1 elprep/2.61 gnuplot/5.0.6 lapack/gcc/64/3.5.0 perl/time-piece/1.31 scala/2.12.0
bam-readcount/1 bwa/0.7.15 elprep/3.0 go/1.9 mothur/1.39.1 picard-tools/1.78 seqff/1
basespace-invaders/1.0.0 bwa/0.7.16a elprep/3.01 hdf5/1.6.10 nanonet/1 picard-tools/2.7.1 singularity/2.2.1
basespace-python/1.0.0 bwa/0.7.5a emboss/6.6.0 hdf5_18/1.8.14 ncbi/eutils/2016-11-22 puppet/3.7.5 slurm/14.11.11
bcftools/1.3.1 canu/1.4 ensembl-tools/86 homer/4.9 netperf/2.6.0 R/3.2.2 snpeff/4
bcl2fastq/2.17 cellranger/1.3.1 excelcompare/0.6.1 hpl/2.1 openblas/dynamic/0.2.14 R/3.2.4 star/2.5.2b
beagle/21jan17 cmgui/7.1 fastqc/0.11.5 htseq/0.6.1p1 openlava/3.0 rdp-classifier/2.6 sun-jre/7
beagle/3.3.2 crispresso/1 fastx_toolkit/0.0.13 htslib/1.3.2 openmpi/gcc/64/1.8.5 rdptools/1 tabix/0.2.6
bedtools/2.17.0 cufflinks/2.2.1 flash/1.2.11 igvtools/2.3.78 pandoc/1.16.0.2 rmats/3.2.5 tophat/2.1.1
blas/gcc/64/3.5.0 cutadapt/1.11 gatk/3.1.1 iozone/3_430 penncnv/1.0.3 sambamba/0.6.6 ucsc/utils/v432
blast/2.5.0+ default-environment gatk/3.6 iozone/3_471 perl/5.16.3 samstat/1.5.1 vcfsorter/1
blat/35 dos2unix/7.1 gdb/7.9 java/7.0.25 perl/5.24.1 samtools/0.1.19 vcftools/1
bonnie++/1.97.1 EasyBuild genomicsimla/1.1.3 java/8.0.111 perl/config-simple/4.59 samtools/1.3.1 vep/90
bowtie/1.1.2 ea-utils/27 GNUparallel/20160822 jdk/jdk1.8.0_66 perl/test-simple/1,001014 samtools/1.6 zlib/1.2.8



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