Create config.sh and TODO.org

TODO.org

+* Ajouter messages d'erreur
+* Ecrire la doc
+** Ajouter dans la doc que Tred doit être ouvert dans virtualenv
+*  Mode transfert
+* Brancher EHDN et outlier
+* Ajourer EHDN dans GetResults

config.sh

+#! /bin/sh
+
+### ASDP pipeline###
+## Version: 0.0.1
+## License; AGPLv3
+## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Description: configuration file
+
+INPUTDIR="/archive/gad/shared/bam_new_genome_temp"
+OUTPUTDIR="/work/gad/shared/analyse/STR/pipeline"
+
+# Valid values: "sge"
+INFRA=sge
+
+# Variables specific to SGE
+TRANSFER_QUEUE=transfer
+COMPUTE_QUEUE=batch
+TRANSFER=yes #FIXME attention, changer aussi le delete +++
+
+# Tools
+PARALLEL="/work/gad/shared/bin/parallel/parallel-20150522-1.el7.cern/bin/parallel"
+PARALLEL_JOB_COUNT="16"
+
+EH="/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter"
+EH_VARIANT_CATALOG="/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json"
+
+TREDPARSE="/work/gad/shared/bin/tredparse/Tredparse-20190901/bin/tred.py"
+TREDPARSE_VENV="/work/gad/shared/bin/tredparse/Tredparse-20190901/bin/activate" # To load Tredparse in a virtual environment
+
+GANGSTR="/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR"
+GANGSTR_REGIONS="/work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed"
+
+EHDN="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
+EHDN_OUTLIER="/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
+
+REF="/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
+
+
+
+