Skip to content
Projects
Groups
Snippets
Help
This project
Loading...
Sign in / Register
Toggle navigation
S
STR
Project
Project
Details
Activity
Cycle Analytics
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Charts
Issues
0
Issues
0
List
Board
Labels
Milestones
Merge Requests
0
Merge Requests
0
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Charts
Wiki
Wiki
Snippets
Snippets
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Charts
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
Anne-Sophie Denommé-Pichon
STR
Commits
e31af448
Commit
e31af448
authored
Jun 21, 2020
by
Anne-Sophie Denommé-Pichon
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Fix comment in pipeline.sh
parent
22d3c074
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
7 additions
and
5 deletions
+7
-5
README.md
README.md
+5
-3
TODO.org
TODO.org
+1
-1
pipeline.sh
pipeline.sh
+1
-1
No files found.
README.md
View file @
e31af448
...
...
@@ -7,8 +7,10 @@
-
Description: How to launch scripts to get STR genotype from genomes on all the locus tested
1.
Fill the configuration file
`config.sh`
.
2.
Create
`samples.list`
(bam file names without .bam)
3.
Launch
`launch_pipeline.sh`
:
`nohup ./launch_pipeline.sh samples.list &`
. Dependencies :
2.
Create
`samples.list`
(bam file names without .bam).
For now, scripts have to be launched from the clone directory.
3.
Launch
`launch_pipeline.sh`
:
`nohup ./launch_pipeline.sh samples.list &`
. Dependencies:
-
`config.sh`
-
`samples.list`
-
`pipeline.sh`
...
...
@@ -18,7 +20,7 @@
-
`wrapper_gangstr.sh`
-
`wrapper_transfer.sh`
-
`wrapper_tredparse.sh`
4.
Optional: launch
`launch_pipeline_ehdn_outlier.sh`
:
`nohup ./launch_pipeline_ehdn_outlier.sh &`
. Dependencies
:
4.
Optional: launch
`launch_pipeline_ehdn_outlier.sh`
:
`nohup ./launch_pipeline_ehdn_outlier.sh &`
. Dependencies:
-
`config.sh`
-
`pipeline_ehdn_outlier.sh`
-
`wrapper_ehdn_outlier.sh`
...
...
TODO.org
View file @
e31af448
- [ ] Ajouter la possibilité de lancer le pipeline depuis n'importe quel répertoire et pas seulement celui où se trouvent les scripts
- [ ] Ajouter messages d'erreur
- [ ] Ecrire la doc
- [ ] Ajouter dans la doc que Tred doit être ouvert dans virtual
...
...
@@ -16,7 +17,6 @@
- [ ] Faire un launcher pour lancer getResults dans SGE
- [X] Ajouter la possibilité de faire tourner getResults sur une liste d'échantillons donnée (actuellement, glob *)
- [X] Créer le répertoire results automatiquement (sans la date)
- [ ] Ajouter la possibilité de lancer le pipeline depuis n'importe quel répertoire et pas seulement celui où se trouvent les scripts
- [ ] Créer un script pour faire le ménage après le passage de SGE
- [ ] Possibilité de choisir les outils à utiliser (par exemple, option pour ne pas utiliser GangSTR)
- [X] Gérer l'absence de queue transfer
pipeline.sh
View file @
e31af448
...
...
@@ -33,7 +33,7 @@ OUTPUTDIR="$OUTPUTDIR/$SAMPLE"
TRANSFER_JOB
=
""
WD
=
"
$(
dirname
"
$(
readlink
-f
"
$0
"
)
"
)
"
Transfer bam and bai from archive to work
#
Transfer bam and bai from archive to work
if
[
"x
$TRANSFER
"
=
"xyes"
]
then
mkdir
-p
"
$OUTPUTDIR
"
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment