Merge pull request #1055 from maxplanck-ie/KS

docs
maxplanck-ie · Sep 10, 2024 · 3f43eb2 · 3f43eb2
2 parents 3f98cd8 + a2568b2
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diff --git a/docs/content/setting_up.rst b/docs/content/setting_up.rst
@@ -63,7 +63,7 @@ or for the pytests:
 Configuring snakePipes
 ----------------------
 
-Finally, at least one file (``defaults.yaml``) should be modified to match your compute infrastructure. The location of this file can be found out by executing:
+Finally, config files ``defaults.yaml`` and snakemake profile should be modified to match your compute infrastructure. The location of this file can be found out by executing:
 
 .. code:: bash
 
@@ -86,7 +86,7 @@ If you want to use the snakepipes_genericprofile, make sure to review the follow
 
  * ``module load slurm &&`` - could be omitted
  * ``resources.partition`` - set to your slurm partition
- * ``conda-prefix`` - set to your preferred location where snakePipes environments should be stored
+ * ``conda-prefix`` - set to your preferred location where snakePipes environments should be stored. You can set this value by running `snakePipes config --condaEnvDir` and providing the respective path.
  * ``resources`` - make sure default resources make sense for your infrastructure
  * ``ccancel.sh`` - refers to the ccancel.sh file inside the profile directory and contains instructions on how to kill submitted jobs (on failure / interruption of snakemake). The module command could be omitted here as before
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -45,7 +45,8 @@ Quick start
 
 * Download genome fasta and annotations for an your organism, and build indexes, Check in :ref:`createIndices`
 
-* Configure snakePipes with paths to organism and cluster configs on your system using snakePipes config. For detailed information, run:
+* Configure snakePipes with paths to organism and snakemake configs on your system using snakePipes config. Importantly, take care to set `--condaEnvDir` parameter, which defaults to `/tmp`. 
+  For detailed information, run:
 
 .. code:: bash