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Cedric Midoux
deepomics16S
Commits
2ae511c6
Commit
2ae511c6
authored
Feb 23, 2021
by
Cedric Midoux
Browse files
LOGS
parent
d7c2d7c7
Changes
6
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.gitignore
View file @
2ae511c6
.log
/
LOGS
/
.snakemake/
DATA/
work/
report/
.Rproj.user
.Rhistory
DADA2.Rproj
0 → 100644
View file @
2ae511c6
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
RunSnake.sh
View file @
2ae511c6
...
...
@@ -3,7 +3,7 @@ export PYTHONPATH=''
source
/usr/local/genome/Anaconda2-5.1.0/etc/profile.d/conda.sh
conda activate snakemake-5.7.4
mkdir
-p
./.log/out/ ./.log/err
/
mkdir
-p
LOGS
/
snakemake
\
--snakefile
$1
\
...
...
cluster.json
View file @
2ae511c6
{
"__default__"
:
{
"out"
:
"
./.log/out
/"
,
"err"
:
"
./.log/err
/"
,
"queue"
:
"
short
.q"
,
"out"
:
"
LOGS
/"
,
"err"
:
"
LOGS
/"
,
"queue"
:
"
maiage
.q"
,
"cluster"
:
""
}
}
global.smk
View file @
2ae511c6
...
...
@@ -15,7 +15,8 @@ rule all:
"report/clusters_metrics.html",
"report/affiliations_metrics.html",
"report/abundance.biom",
"report/abundance.tsv"
"report/abundance.tsv",
"report/tree.nwk"
include: "quality.smk"
include: "preprocess.smk"
...
...
qsubSnake.sh
View file @
2ae511c6
mkdir
-p
./.log/out/ ./.log/err
/
qsub
-V
-cwd
-o
./.log/out/
-e
./.log/err
/
-q
maiage.q,long.q
-N
`
basename
$1
`
RunSnake.sh
$1
mkdir
-p
LOGS
/
qsub
-V
-cwd
-o
LOGS/
-e
LOGS
/
-q
maiage.q,long.q
-N
`
basename
$1
`
RunSnake.sh
$1
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