Commit be0cdf70 authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

Update README.md

parent 65b247e1
......@@ -26,7 +26,7 @@ To try the workflow, just run the two following command lines.
conda activate microSysMics
# The following awk command just set absolute filepaths in the test manifest file. To run only once.
awk -v P="$(pwd)" 'BEGIN{FS=",";}NR==1{print $1","$2","$3;}NR>1{print $1","P"/"$2","$3;}' test/manifest.csv > test/manifest.tmp && mv test/manifest.tmp test/manifest.csv
snakemake -p --use-conda
snakemake -p -k --use-conda
~~~
......@@ -38,10 +38,10 @@ If using a cluster, the call is slightly different :
conda activate microSysMics
# The following awk command just set absolute filepaths in the test manifest file. To run only once.
awk -v P="$(pwd)" 'BEGIN{FS=",";}NR==1{print $1","$2","$3;}NR>1{print $1","P"/"$2","$3;}' test/manifest.csv > test/manifest.tmp && mv test/manifest.tmp test/manifest.csv
snakemake -p --use-conda --latency-wait 60 --cluster "qsub" --jobs 40 --jobscript microSysMics.sh
snakemake -p -k --use-conda --latency-wait 60 --cluster "qsub" --jobs 40 --jobscript microSysMics.sh
~~~
For some reason, on our cluster, we need a wrapper to encapsulate the jobs (specified by the **--jobscript** option). It's also worth noting that we must indicate output logs directory (that must me created beforhand) or snakemake will crash. Some specific configuration may be needed for your own cluster.
For some reason, on our cluster, we need a wrapper to encapsulate the jobs (specified by the **--jobscript** option). Some specific configuration may be needed for your own cluster.
## Running for real
......@@ -83,9 +83,19 @@ Once the configuration file is written, we can run the workflow.
~~~
conda activate microSysMics
snakemake -p --use-conda --configfile config_user.json
snakemake -p -k --use-conda --configfile config_user.json
~~~
### Build report
Once your analysis is done, you can generate an html report as follows.
~~~
snakemake build_report -p -k --use-conda --configfile config_user.json
~~~
This command will create a *report.tar.gz* archive in your output directory.
Extract it and open the microSysMics.html file in your favorite web browser, you will then have access to your analysis results through it.
### use Docker
......
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