GDC software stack
The GDC software stacks (CentOS) listed below are obsolete and not compatible with the new Ubuntu setup. You can find an overview on the Ubuntu software stack on this wiki page which also contains many modules that were part of the GDC software stack in the old CentOS setup.
GDC¶
The Genetic Diversity Centre (GDC) of ETH Zurich is a well established knowledge and technology platform of the D-USYS Department. It offers a well equipped user-lab and customised bioinformatic support and services for research related to genetic and genomic diversity in a wide range of organisms. It offers customized support for research projects in the field of genetic diversity with a wide range of technical expertise and a dynamic, well-connected team. The GDC is open to all academic institutions within Switzerland.
Contact¶
Genetic Diversity Centre
Universitätstrasse 16
CHN E 55.1
8092 Zurich / Switzerland
http://www.gdc.ethz.ch
Software stack on Euler¶
The GDC bioninformatics software stack on Euler was installed as part of GDCs SIS subscription. It is a collection of tools and libraries, selected by the GDC team. The GDC team builds runscripts and workflows based on the tools of this software stack. The tools are available to all cluster users, but if you are interested in runscripts or workflows, then please contact the GDC team.
Please note that the GDC software stack is part of the old Euler software stack and can not be used together with tools from the new software stack.
Old vs. new software stack¶
Please note that the GDC software stack was setup as part of the old Euler software stack. Meanwhile, a newer software stack is provided. You can switch back and forth between the old and the new software stack within the current terminal, but you cannot mix tools from both software stacks. There is also the option of setting a permanent default for the software stack that is initialized upon login. You can change this default at any time.
Available tools and libraries (new software stack)¶
This is work in progress. We will provide soon the list of bioinformatics tools available in the new software stack, including the module commands. The new software stack features the concept of toolchains and a module hierarchy using LMOD modules. A toolchain is a combination of a compiler and eventually an MPI library. Packages are then compiled for one or more toolchains. Due to the module hierarchy, you can only load one compiler at the time and you can only load packages that are available for the compiler module you have loaded (with the exceptions of Core modules, which can be loaded for all available compilers). This is to prevent conflicts that users can encounter when mixing tools that were compiled with different compiler versions. A full overview on all available modules (not just bioinformatics) is provided as well on our wiki.
The list provides the information for which toolchain (GCC 4.8.5, 6.3.0, 8.2.0 and Intel 19.1.0) a software is available and how the module command looks like. Please note that you need to have the corresponding GCC version loaded to be able to load the module of the bioinformatics tool. For instance, the freebayes 1.3.5 module is available for the GCC 6.3.0 and 8.2.0 toolchain but not for GCC 4.8.5. You can load the module in the GCC 6.3.0 toolchain with the command
module load gcc/6.3.0 freebayes/1.3.5
and for the GCC 8.2.0 toolchain with the command
module load gcc/8.2.0 freebayes/1.3.5
Please note that if you already have the corresponding gcc module loaded, then you don't need to load it again and can directly load the freebayes module.
Application |
GCC 4.8.5 |
GCC 6.3.0 |
GCC 8.2.0 |
Intel 19.1.0 |
Module load command |
|---|---|---|---|---|---|
admixtools 7.0.2 |
module load admixtools/7.0.2 |
||||
amrfinder 3.11.2 |
module load openmpi/4.1.4 amrfinder/3.11.2 |
||||
angsd 0.921 |
module load angsd/0.921 |
||||
angsd 0.925 |
module load angsd/0.925 |
||||
angsd 0.940 |
module load angsd/0.940 |
||||
armadillo 9.700.2 |
module load openmpi/4.0.2 armadillo/9.700.2 |
||||
assembly-stats 1.0.1 |
module load assembly-stats/1.0.1 |
||||
ATLAS 0.9.9 |
module load openmpi/4.1.4 atlas/0.9.9 |
||||
augustus 3.4.0 |
module load augustus/3.4.0 |
||||
bamstats 1.25 |
module load bamstats/1.25 |
||||
bamtools 2.5.1 |
module load bamtools/2.5.1 |
||||
bamutil 1.0.13 |
module load bamutil/1.0.13 |
||||
bamutil 1.0.15 |
module load bamutil/1.0.15 |
||||
bbmap 37.36 |
module load bbmap/37.36 |
||||
bbmap 39.05 |
module load bbmap/39.05 |
||||
bcftools 1.15.1 |
module load bcftools/1.15.1 |
||||
bcftools 1.16 |
module load bcftools/1.16 |
||||
bcl2fastq 2.20.422 |
module load bcl2fastq/2.20.422 |
||||
beagle 3.3.2 |
module load beagle/3.3.2 |
||||
beagle 4.1 |
module load beagle/4.1 |
||||
beagle 5.1 |
module load beagle/5.1 |
||||
beagle 5.4 |
module load beagle/5.4 |
||||
beast2 2.4.6 |
module load beast2/2.4.6 |
||||
beast2 2.5.2 |
module load beast2/2.5.2 |
||||
bedops 2.4.36 |
module load bedops/2.4.36 |
||||
bedtools2 2.26.0 |
module load bedtools2/2.26.0 |
||||
bedtools2 2.27.1 |
module load bedtools2/2.27.1 |
||||
bedtools2 2.29.2 |
module load bedtools2/2.29.2 |
||||
bedtools2 2.30.0 |
module load bedtools2/2.30.0 |
||||
bismark 0.19.0 |
module load bismark/0.19.0 |
||||
blast+ 2.9.0 |
module load blast-plus/2.9.0 |
||||
blat 35 |
module load blat/35 |
||||
blat 36 |
module load blat/36 |
||||
bowtie 1.2 |
module load bowtie/1.2 |
||||
bowtie 1.3.0 |
module load bowtie/1.3.0 |
||||
bowtie 1.3.1 |
module load bowtie/1.3.1 |
||||
bowtie2 2.3.4.1 |
module load bowtie2/2.3.4.1 |
||||
bowtie2 2.3.5.1 |
module load bowtie2/2.3.5.1 |
||||
bowtie2 2.4.4 |
module load bowtie2/2.4.4 |
||||
bowtie2 2.5.1 |
module load bowtie2/2.5.1 |
||||
breseq 0.30.1 |
module load breseq/0.30.1 |
||||
breseq 0.32.0 |
module load breseq/0.32.0 |
||||
breseq 0.34.1 |
module load breseq/0.34.1 |
||||
breseq 0.36.0 |
module load breseq/0.36.0 |
||||
bwa 0.7.12 |
module load bwa/0.7.12 |
||||
bwa 0.7.15 |
module load bwa/0.7.15 |
||||
bwa 0.7.17 |
module load bwa/0.7.17 |
||||
canu 1.9 |
module load canu/1.9 |
||||
cd-hit 4.6.8 |
module load cdhit/4.6.8 |
||||
checkm 1.1.2 |
module load checkm/1.1.2 |
||||
clustalo 1.2.4 |
module load clustalo/1.2.4 |
||||
clustalw 2.1 |
module load clustalw/2.1 |
||||
diamond 0.9.14 |
module load diamond/0.9.14 |
||||
diamond 0.9.22 |
module load diamond/0.9.22 |
||||
diamond 0.9.24 |
module load diamond/0.9.24 |
||||
diamond 0.9.28 |
module load diamond/0.9.28 |
||||
diamond 2.0.6 |
module load diamond/2.0.6 |
||||
emboss 6.6.0 |
module load emboss/6.6.0 |
||||
exonerate 2.4.0 |
module load exonerate/2.4.0 |
||||
fasta 36.3.8g |
module load fasta/36.3.8g |
||||
fastani 1.33 |
module load fastani/1.33 |
||||
fastme 2.1.5.1 |
module load fastme/2.1.5.1 |
||||
fastp 0.23.2 |
module load fastp/0.23.2 |
||||
fastqc 0.11.4 |
module load fastqc/0.11.4 |
||||
fastqc 0.11.5 |
module load fastqc/0.11.5 |
||||
fastqc 0.11.9 |
module load fastqc/0.11.9 |
||||
fastqscreen 0.11.2 |
module load fastq-screen/0.11.2 |
||||
fastqscreen 0.11.2 |
module load fastq-screen/0.15.3 |
||||
fasttree 2.1.11 |
module load fasttree/2.1.11 |
||||
fastx_toolkit 0.0.14 |
module load fastx-toolkit/0.0.14 |
||||
flash 1.2.11 |
module load flash/1.2.11 |
||||
fraggenescan 1.31 |
module load fraggenescan/1.31 |
||||
freebayes 1.3.5 |
module load freebayes/1.3.5 |
||||
freebayes 1.3.7 |
module load freebayes/1.3.7 |
||||
gatk 4.0.4.0 |
module load gatk/4.0.4.0 |
||||
gatk 4.0.10.0 |
module load gatk/4.0.10.0 |
||||
gatk 4.1.1.0 |
module load gatk/4.1.1.0 |
||||
gatk 4.2.1.0 |
module load gatk/4.2.1.0 |
||||
gatk 4.2.6.1 |
module load gatk/4.2.6.1 |
||||
gatk 4.4.0.0 |
module load gatk/4.4.0.0 |
||||
gemma 0.98.5 |
module load gemma/0.98.5 |
||||
guppy (CPU) 5.0.16 |
module load guppy-cpu/5.0.16 |
||||
hisat2 2.1.0 |
module load hisat2/2.1.0 |
||||
hisat2 2.2.1 |
module load hisat2/2.2.1 |
||||
hmmer 3.1 b2 |
module load openmpi/4.0.2 hmmer/3.1b2 |
||||
hmmer 3.3.2 |
module load openmpi/4.1.4 hmmer/3.3.2 |
||||
htslib 1.2 |
module load htslib/1.2 |
||||
htslib 1.3.1 |
module load htslib/1.3.1 |
||||
htslib 1.6 |
module load htslib/1.6 |
||||
htslib 1.7 |
module load htslib/1.7 |
||||
htslib 1.10.2 |
module load htslib/1.10.2 |
||||
htslib 1.12 |
module load htslib/1.12 |
||||
htslib 1.15.1 |
module load htslib/1.15.1 |
||||
htslib 1.16 |
module load htslib/1.16 |
||||
hyphy 2.3.14 |
module load hyphy/2.3.14 |
||||
idba 1.1.3 |
module load idba/1.1.3 |
||||
itsx 1.1.3 |
module load openmpi/4.0.2 itsx/1.1.3 |
||||
lastz 1.04.03 |
module load lastz/1.04.03 |
||||
mafft 7.221 |
module load mafft/7.221 |
||||
mafft 7.490 |
module load mafft/7.490 |
||||
mash 2.3 |
module load mash/2.3 |
||||
mcl 14.137 |
module load mcl/14-137 |
||||
megahit 1.1.4 |
module load megahit/1.1.4 |
||||
miniasm 2018-3-30 |
module load miniasm/2018-3-30 |
||||
minimap2 2.17 |
module load minimap2/2.17 |
||||
mosdepth 0.3.3 |
module load mosdepth/0.3.3 |
||||
motus 3.1 |
module load motus/3.1 |
||||
muscle 3.8.31 |
module load muscle/3.8.31 |
||||
muscle 3.8.1551 |
module load muscle/3.8.1551 |
||||
picard 2.18.14 |
module load picard/2.18.14 |
||||
picard 2.23.2 |
module load picard/2.23.2 |
||||
picard 2.25.7 |
module load picard/2.25.7 |
||||
picard 3.1.1 |
module load picard/3.1.1 |
||||
plink 1.9 beta6.18 |
module load plink/1.9-beta6.18 |
||||
pplacer 1.1 alpha19 |
module load pplacer/1.1.alpha19 |
||||
primer3 2.4.0 |
module load primer3/2.4.0 |
||||
prinseq-lite 0.20.4 |
module load prinseq-lite/0.20.4 |
||||
prodigal 2.6.3 |
module load prodigal/2.6.3 |
||||
raxml 8.2.12 |
module load openmpi/4.0.2 raxml/8.2.12 |
||||
raxml-ng 1.2.0 |
module load openmpi/4.1.4 raxml-ng/1.2.0 |
||||
sambamba 0.8.1 |
module load sambamba/0.8.1 |
||||
samblaster 0.1.24 |
module load samblaster/0.1.24 |
||||
samtools 1.2 |
module load samtools/1.2 |
||||
samtools 1.6 |
module load samtools/1.6 |
||||
samtools 1.10 |
module load samtools/1.10 |
||||
samtools 1.12 |
module load samtools/1.12 |
||||
samtools 1.15.1 |
module load samtools/1.15.1 |
||||
samtools 1.16.1 |
module load samtools/1.16.1 |
||||
seqkit 0.16.1 |
module load seqkit/0.16.1 |
||||
seqkit 2 .4.0 |
module load seqkit/2.4.0 |
||||
seqtk 1.2 |
module load seqtk/1.2 |
||||
seqtk 1.3 |
module load seqtk/1.3 |
||||
spades 3.6.2 |
module load spades/3.6.2 |
||||
spades 3.10.0 |
module load spades/3.10.0 |
||||
spades 3.11.1 |
module load spades/3.11.1 |
||||
spades 3.14.0 |
module load spades/3.14.0 |
||||
spades 3.15.4 |
module load spades/3.15.4 |
||||
sra toolkit 2.8.1 |
module load sra-toolkit/2.8.1 |
||||
sra toolkit 2.8.2-1 |
module load sra-toolkit/2.8.2-1 |
||||
sra toolkit 2.9.2 |
module load sra-toolkit/2.9.2 |
||||
sra toolkit 2.10.5 |
module load sra-toolkit/2.10.5 |
||||
stacks 2.59 |
module load stacks/2.59 |
||||
stacks 2.65 |
module load stacks/2.65 |
||||
star 2.5.3 a |
module load star/2.5.3a |
||||
star 2.7.2 d |
module load star/2.7.2d |
||||
star 2.7.9 a |
module load star/2.7.9a |
||||
subread 2.0.1 |
module load subread/2.0.1 |
||||
subread 2.0.3 |
module load subread/2.0.3 |
||||
tophat 2.1.2 |
module load tophat/2.1.2 |
||||
trimgalore 0.6.6 |
module load trimgalore/0.6.6 |
||||
trimmomatic 0.35 |
module load trimmomatic/0.35 |
||||
trimmomatic 0.36 |
module load trimmomatic/0.36 |
||||
trimmomatic 0.38 |
module load trimmomatic/0.38 |
||||
usearch 11.0.667 |
module load usearch/11.0.667 |
||||
vcftools 0.1.14 |
module load vcftools/0.1.14 |
||||
vcftools 0.1.16 |
module load vcftools/0.1.16 |
||||
velvet 1.2.10 |
module load velvet/1.2.10 |
||||
vsearch 2.14.1 |
module load vsearch/2.14.1 |