Merge pull request #90 from NBISweden/gerp

Fix bugs in the GERP step of the pipeline

Snakefile

@@ -2,7 +2,6 @@
 # This is the Snakefile of the GenErode pipeline for historical or       #
 # ancient and modern samples to study patterns of genome erosion         #
 #                                                                        #
-# Pipeline version 0.6.0                                                 #
 #                                                                        #
 # Written by Verena Kutschera, Marcin Kierczak and Tom van der Valk      #
 # Email: generode@nbis.se                                                #
@@ -17,6 +16,7 @@
 # (https://github.com/NBISweden/GenErode/wiki).
 ###
 
+generode_version = "0.6.2"
 
 ##########################################################################
 ########################### STEPS TO INCLUDE #############################

config/config.yaml

@@ -1,6 +1,6 @@
 #################################################################
 #################################################################
-# Configuration settings for the GenErode pipeline 0.6.0        #
+# Configuration settings for the GenErode pipeline 0.6.2        #
 # for ancient or historical samples, and modern samples         #
 #################################################################
 #################################################################

config/slurm/README.md

@@ -10,6 +10,12 @@ module load PDC bioinfo-tools conda apptainer tmux
 but the equivalent tool `screen` is pre-installed and does 
 not need to be loaded. 
 
+> Apptainer (former singularity) will store its cache per 
+default in your home directory which will quickly run out of 
+storage space. You can tell it to use your `scratch` instead, a 
+temporary directory with unlimited space by adding this row 
+to your `~/.bashrc`: `export APPTAINER_CACHEDIR=$PDC_TMP`.
+
 2) After cloning the repository, change permissions for the 
 Snakefile:
 
@@ -19,21 +25,19 @@ chmod 755 Snakefile
 
 3) Create the GenErode conda environment or update an earlier 
 version. The latest conda environment contains the Snakemake 
-executor plugin for slurm:
-
-```
-conda env create -f environment.yml -n generode
-```
-
-- If you want to create a conda environment in a different location 
-than your home directory, you can provide a path to a directory 
-for the conda environment to be installed in, and run the following
-command instead of the command above:
+executor plugin for slurm. Since home directories on Dardel 
+are limited in storage space, you need to create a directory in 
+your storage project for the conda environment to be installed 
+in, and run the following command instead of the command above:
 
 ```
 conda env create -f environment.yml -p /cfs/klemming/projects/supr/sllstore.../generode
 ```
 
+> Note that you can save storage space in your storage project 
+on Dardel by creating a common GenErode conda environment for 
+several people. 
+
 4) Copy the configuration file `config/slurm/profile/config_plugin_dardel.yaml` 
 to `slurm/config.yaml`. This file specifies Snakemake and apptainer 
 parameters that are used to run the pipeline, as well as compute 
@@ -60,16 +64,9 @@ resources specified under`default-resources`.
 
 - Open a tmux session (alternatively, you can use screen)
 
-- Activate the GenErode conda environment (created or updated 
-from `environment.yml`):
-
-```
-conda activate generode
-```
-
-If you have created the conda environment in a different directory 
-than your home directory, run the following commands, replacing the 
-path to the location of the conda environment accordingly:
+- Activate the GenErode conda environment with the 
+following commands, replacing the path to the location of 
+the conda environment accordingly:
 
 ```
 export CONDA_ENVS_PATH=/cfs/klemming/home/.../