SOFT : OrthoFinder
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Site du soft: https://github.com/davidemms/OrthoFinder
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LICENSE:
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GPL-v3.0

See software documentation for more informations.

Location: /usr/local/bioinfo/src/OrthoFinder
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Load binaries and environment:
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-> Version v2.2.1

Load dependencies:
module load bioinfo/ncbi-blast-2.6.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.19

If needed ( Trees from MSA):
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.2.1

-> Version v2.2.3

Load dependencies:
module load bioinfo/ncbi-blast-2.6.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.22

If needed ( Trees from MSA):
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.2.3

-> Version v2.2.7

Load dependencies:
module load bioinfo/ncbi-blast-2.6.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.22

If needed ( Trees from MSA):
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.2.7

-> Version v2.3.7

Load dependencies:
module load bioinfo/ncbi-blast-2.6.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.19

If needed :
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10 bioinfo/muscle3.8.31

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.3.7

-> Version v2.3.12

Load dependencies:
module load bioinfo/ncbi-blast-2.10.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.19

If needed :
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10 bioinfo/muscle3.8.31

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.3.12

-> Version v2.4.0

Load dependencies:
module load bioinfo/ncbi-blast-2.10.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.19

If needed :
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10 bioinfo/muscle3.8.31 bioinfo/mmseqs2-v9-d36de

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.4.0

-> Version v2.5.2

Load dependencies:
module load bioinfo/ncbi-blast-2.10.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.19

If needed :
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10 bioinfo/muscle3.8.31 bioinfo/mmseqs2-v9-d36de

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.5.2

-> Version v2.5.4

Load dependencies:
module load bioinfo/ncbi-blast-2.10.0+ bioinfo/fastme-2.1.6.1 bioinfo/dlcpar-1.0 bioinfo/mcl-14-137 bioinfo/diamond-v0.9.19

If needed :
module loadbioinfo/mafft-7.313 bioinfo/FastTree-2.1.10 bioinfo/muscle3.8.31 bioinfo/mmseqs2-v9-d36de

and  load OrthoFinder:
module load bioinfo/OrthoFinder-2.5.4

-> Version v2.5.5
#Need Miniconda
module load system/Miniconda3
module load bioinfo/OrthoFinder/2.5.5

To unload module, unload  in order:

module unload bioinfo/OrthoFinder/2.5.5
module unload system/Miniconda3

Warning! By default 128 threads are used on the node. Don't forget to adjust -t and -a  option of orthofinder command and --cpus-per-task option for Slurm.


Example directory for use on cluster:
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/usr/local/bioinfo/src/OrthoFinder/example_on_cluster

To submit: sbatch test_OrthoFinder-2.2.1.sh

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.