From bf4f0c4331c324195400f2abc775e8b48c135562 Mon Sep 17 00:00:00 2001
From: Malte Herold <malte.herold@uni.lu>
Date: Mon, 13 Apr 2015 16:28:14 +0200
Subject: [PATCH] added dependencies for gaia
---
conf/gaia_PREPROCESSING_modules.sh | 9 ---------
conf/userconfig.imp.json | 4 ++--
modules_to_preload.sh | 27 +++++++++++++++++++++++++++
3 files changed, 29 insertions(+), 11 deletions(-)
delete mode 100644 conf/gaia_PREPROCESSING_modules.sh
create mode 100644 modules_to_preload.sh
diff --git a/conf/gaia_PREPROCESSING_modules.sh b/conf/gaia_PREPROCESSING_modules.sh
deleted file mode 100644
index ad0af30..0000000
--- a/conf/gaia_PREPROCESSING_modules.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash -l
-
-module load BWA
-module load SAMtools
-module load BEDTools
-module load OpenBLAS
-module load Boost/1.53.0-ictce-5.3.0
-
-module list
diff --git a/conf/userconfig.imp.json b/conf/userconfig.imp.json
index 6ed4704..795c559 100644
--- a/conf/userconfig.imp.json
+++ b/conf/userconfig.imp.json
@@ -3,7 +3,7 @@
"threads": 4
},
"Preprocessing": {
- "pre": "echo '//LOADING PREPROCESSING MODULE: You can write custom shell commands here' && source /home/users/snarayanasamy/repositories/IMP/conf/gaia_PREPROCESSING_modules.sh",
+ "pre": "echo '//LOADING PREPROCESSING MODULE: You can write custom shell commands here' ",
"filtering": false,
"trimmomatic": {
"jarfile": "/mnt/nfs/projects/ecosystem_biology/local_tools/Trimmomatic-0.32/trimmomatic-0.32.jar",
@@ -18,7 +18,7 @@
}
},
"Assembly": {
- "pre": "echo '//LOADING ASSEMBLY MODULE' && source /home/users/mherold/TOOLS/IMP/conf/gaia_ASSEMBLY_modules.sh"
+ "pre": "echo '//LOADING ASSEMBLY MODULE'"
},
"Analysis": {
"pre": "echo '//LOADING ANALYSIS MODULE'"
diff --git a/modules_to_preload.sh b/modules_to_preload.sh
new file mode 100644
index 0000000..30d4c0b
--- /dev/null
+++ b/modules_to_preload.sh
@@ -0,0 +1,27 @@
+#!/bin/bash -l
+
+
+module load Python
+source env/bin/activate
+
+module load MEGAHIT
+module load BWA
+module load SAMtools
+module load BEDTools
+module load OpenBLAS
+module load Boost/1.53.0-ictce-5.3.0
+
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/idba-1.1.1.icc/bin
+
+module load CAP3
+
+#symbolic links for prokka db
+module load prokka
+
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/tabix-0.2.6
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/gkno_launcher/tools/freebayes/bin
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/bin
+export PERL5LIB=$PERL5LIB:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/perl
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/Platypus_0.7.9.1
+
+module list
--
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