From 1b3f9df2809e7fa7b8dd2bd7e9da846f26e5c7b4 Mon Sep 17 00:00:00 2001
From: ameyner2 <alison.meynert@igmm.ed.ac.uk>
Date: Wed, 7 Apr 2021 09:21:05 +0100
Subject: [PATCH] Fixed qsub commas
---
docs/SOP_archiving.md | 18 ++++--------------
1 file changed, 4 insertions(+), 14 deletions(-)
diff --git a/docs/SOP_archiving.md b/docs/SOP_archiving.md
index 7cab069..5c17c13 100644
--- a/docs/SOP_archiving.md
+++ b/docs/SOP_archiving.md
@@ -44,9 +44,7 @@ cd /home/u035/project/trio_whole_exome/analysis/logs
```
qsub -v \
- PROJECT_ID=$project_id,\
- VERSION=$version,\
- CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
+ PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
-N trio_whole_exome_cram_compression.$project_id -J 1-${X} \
/home/u035/project/scripts/submit_trio_wes_cram_compression.sh
```
@@ -55,9 +53,7 @@ qsub -v \
```
qsub -v \
- PROJECT_ID=$project_id,\
- VERSION=$version,\
- CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
+ PROJECT_ID=$project_id,VERSION=$version,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
-N trio_whole_exome_checksums.$project_id -J 1-${X} \
/home/u035/project/scripts/submit_trio_wes_checksums.sh
cd ../output
@@ -69,10 +65,7 @@ wc -l *$project_id*/md5sum.txt
```
priority_dirs=ddmmyyyy #:ddmmyyyy
qsub -v \
- PROJECT_ID=$project_id,\
- VERSION=$version,\
- PRIORITY_DIRS=$priority_dirs,\
- CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
+ PROJECT_ID=$project_id,VERSION=$version,PRIORITY_DIRS=$priority_dirs,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
-N trio_whole_exome_priority_and_qc_checksums.$project_id \
/home/u035/project/scripts/submit_trio_wes_priority_and_qc_checksums.sh
```
@@ -81,10 +74,7 @@ qsub -v \
```
qsub -v \
- PROJECT_ID=$project_id,\
- VERSION=$version,\
- PRIORITY_DIRS=$priority_dirs, \
- CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
+ PROJECT_ID=$project_id,VERSION=$version,PRIORITY_DIRS=$priority_dirs,CONFIG_SH=/home/u035/project/scripts/trio_whole_exome_config.sh \
-N trio_whole_exome_archive_project.$project_id \
/home/u035/project/scripts/submit_trio_wes_archive_project.sh
grep -c FAIL trio_whole_exome_archive_project.$project_id*
--
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