SOFT : PALEOMIX
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Site du soft: http://paleomix.readthedocs.io/
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LICENSE:
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GPL-v3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/PALEOMIX
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Load binaries and environment:
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-> Version v1.2.13

module load bioinfo/paleomix_v1.2.13
(to quit:  module unload bioinfo/paleomix_v1.2.13 or module purge)

-> Version v1.2.13.3

module load bioinfo/paleomix_v1.2.13.3
(to quit:  module unload bioinfo/paleomix_v1.2.13.3 or module purge)

-> Version v1.2.13.5

module load bioinfo/paleomix_v1.2.13.5
(to quit:  module unload bioinfo/paleomix_v1.2.13.5 or module purge)


and

For Bam pipelines:
module load bioinfo/adapterremoval-2.2.2 bioinfo/samtools-0.1.19 bioinfo/picard-1.137 bioinfo/bowtie2-2.2.9 bioinfo/bwa-0.7.15  system/R-3.4.3

For Phylogenetic pipeline:
module load bioinfo/samtools-0.1.19 bioinfo/tabix-0.2.5 bioinfo/mafft-7.313 bioinfo/standard-RAxML-8.2.11 compiler/gcc-4.8.5 mpi/openmpi-2.1.2 bioinfo/ExaML-3.0.20

For Zonkey pipeline:
module load system/R-3.4.3 bioinfo/EIG-7.2.1 bioinfo/admixture_linux-1.3.0 bioinfo/plink-1.07-x86_64 bioinfo/standard-RAxML-8.2.11 bioinfo/samtools-0.1.19 bioinfo/treemix-1.13


-> Version v1.3.7

#Need Miniconda3
module load system/Miniconda3
module load bioinfo/paleomix-v1.3.7

Be careful, to unload, not use module purge but in order:

module unload bioinfo/paleomix-v1.3.7
module unload system/Miniconda3


Need to create link in your home:

mkdir -p ~/install/jar_root
ln -s /usr/local/bioinfo/src/Miniconda/Miniconda3/envs/paleomix-v1.3.7_env/share/picard-2.27.4-0/picard.jar ~/install/jar_root/


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

For Bam pipelines: 
cd bam_pipeline
To submit: sbatch test_paleomix_v1.2.13_bam.sh or sbatch test_paleomix_v1.2.13.3_bam.sh or sbatch test_paleomix_v1.2.13.5_bam.sh or sbatch test_paleomix_v1.3.7_bam.sh

For Phylogenetic pipeline:
cd cd phylo_pipeline
To submit: sbatch test_paleomix_v1.2.13_phylo_pipeline.sh

For Zonkey pipeline:
cd zonkey_pipeline/
To submit: sbatch test_paleomix_v1.2.13_zonkey_pipeline.sh

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