From 0d6fe36d66b365df5009a3f26c4297d95907cb65 Mon Sep 17 00:00:00 2001
From: Malte Herold <malte.herold@uni.lu>
Date: Mon, 13 Apr 2015 14:00:29 +0200
Subject: [PATCH] assembly modules step by step
---
conf/gaia_ASSEMBLY_modules.sh | 4 ++++
conf/userconfig.imp.json | 14 +++++++++++---
2 files changed, 15 insertions(+), 3 deletions(-)
create mode 100644 conf/gaia_ASSEMBLY_modules.sh
diff --git a/conf/gaia_ASSEMBLY_modules.sh b/conf/gaia_ASSEMBLY_modules.sh
new file mode 100644
index 0000000..05de29d
--- /dev/null
+++ b/conf/gaia_ASSEMBLY_modules.sh
@@ -0,0 +1,4 @@
+#!/bin/bash -l
+
+#export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/megahit/megahit_v0.2.1
+module load MEGAHIT
diff --git a/conf/userconfig.imp.json b/conf/userconfig.imp.json
index 08e896e..6ed4704 100644
--- a/conf/userconfig.imp.json
+++ b/conf/userconfig.imp.json
@@ -6,11 +6,19 @@
"pre": "echo '//LOADING PREPROCESSING MODULE: You can write custom shell commands here' && source /home/users/snarayanasamy/repositories/IMP/conf/gaia_PREPROCESSING_modules.sh",
"filtering": false,
"trimmomatic": {
- "jarfile": "/mnt/nfs/projects/ecosystem_biology/local_tools/Trimmomatic-0.32/trimmomatic-0.32.jar"
- }
+ "jarfile": "/mnt/nfs/projects/ecosystem_biology/local_tools/Trimmomatic-0.32/trimmomatic-0.32.jar",
+ "datadir": "TEST_DATA",
+ "raws": {
+ "Metagenomics": "MG.R1.5_percent.fq MG.R2.5_percent.fq",
+ "Metatranscriptomics": "MT.R1.5_percent.fq MT.R2.5_percent.fq"
+ },
+ "sample": "test",
+ "outputdir": "build",
+ "db_path": "db"
+ }
},
"Assembly": {
- "pre": "echo '//LOADING ASSEMBLY MODULE'"
+ "pre": "echo '//LOADING ASSEMBLY MODULE' && source /home/users/mherold/TOOLS/IMP/conf/gaia_ASSEMBLY_modules.sh"
},
"Analysis": {
"pre": "echo '//LOADING ANALYSIS MODULE'"
--
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