handle cases when wasp_dir is not provided

Author: aryarm

README.md

@@ -36,4 +36,4 @@ If you have [Anaconda](https://conda.io/docs/user-guide/install/index.html) inst
 - [rtracklayer](https://bioconductor.org/packages/release/bioc/html/rtracklayer.html)
 - [dplyr](https://www.rdocumentation.org/packages/dplyr)
 
-Note that our pipeline uses [WASP](https://www.biorxiv.org/content/early/2014/11/07/011221) (v3.x), which is not available from Anaconda. You must [manually install it](https://github.com/bmvdgeijn/WASP). The `--use-conda` option will automatically handle WASP's dependencies, but you can see the [WASP README](https://github.com/bmvdgeijn/WASP/blob/master/README.md) if you'd like to install these dependencies manually.
+Note that our pipeline uses [WASP](https://github.com/bmvdgeijn/WASP) (v3.x), which is not available from Anaconda. If the pipeline is unable to locate WASP, it will automatically install it. The `--use-conda` option will automatically handle WASP's dependencies, but you can see the [WASP README](https://github.com/bmvdgeijn/WASP/blob/master/README.md) if you'd like to install these dependencies manually.

Snakefiles/Snakefile-WASP

@@ -40,6 +40,9 @@ if 'SAMP_TO_VCF_ID' not in globals():
         return samp_dict
     SAMP_TO_VCF_ID = read_vcf_samples()
 
+# set the wasp_dir if the user hasn't specified one
+if 'wasp_dir' not in config:
+    config['wasp_dir'] = ".snakemake/WASP"
 # set the default SNP H5 dir if the user hasn't specified one
 if 'snp_h5_dir' not in config:
     config['snp_h5_dir'] = "/genotypes/snp_h5"

Snakefiles/Snakefile-counts

@@ -49,6 +49,10 @@ if 'SAMP_TO_VCF_ID' not in globals():
         return samp_dict
     SAMP_TO_VCF_ID = read_vcf_samples()
 
+# set the wasp_dir if the user hasn't specified one
+if 'wasp_dir' not in config:
+    config['wasp_dir'] = ".snakemake/WASP"
+
 
 if not hasattr(rules, 'all'):
     rule all:

configs/config-WASP.yaml

@@ -18,6 +18,7 @@
 
 # If you have downloaded WASP from https://github.com/bmvdgeijn/WASP, specify the path to your WASP directory here
 # Otherwise, specify the location of the directory in which you'd like it installed
+# When this option is not provided, the pipeline will install WASP in your .snakemake directory
 "wasp_dir" : "/iblm/netapp/home/amassarat/bin/WASP"
 
 # directory in which to output all of the output files
@@ -29,6 +30,7 @@
 
 # If you already have SNP HDF5 files, specify the directory of the files here
 # Otherwise, they will be created in this location
+# When this option is not provided, the pipeline will use {output_dir}/genotypes/snp_h5
 "snp_h5_dir" : "out/genotypes/snp_h5"
 
 # what are the maximum number of threads to use for the entire pipeline?

configs/config-counts.yaml

@@ -25,6 +25,7 @@
 
 # If you have downloaded WASP from https://github.com/bmvdgeijn/WASP, specify the path to your WASP directory here
 # Otherwise, specify the location of the directory in which you'd like it installed
+# When this option is not provided, the pipeline will install WASP in your .snakemake directory
 "wasp_dir" : "/iblm/netapp/home/amassarat/bin/WASP"
 
 # Directory in which to output all of the generated files
@@ -36,6 +37,7 @@
 
 # If you already have SNP HDF5 files, specify the directory of the files here
 # Otherwise, they will be created in this location
+# When this option is not provided, the pipeline will use {output_dir}/genotypes/snp_h5
 "snp_h5_dir" : "out/genotypes/snp_h5"
 
 # what are the maximum number of threads to use for each rule in the pipeline?