Add absolute path for the environments

cbg-ethz · Apr 6, 2020 · 2ef84bc · 2ef84bc
1 parent 8783c72
commit 2ef84bc
Showing 1 changed file with 11 additions and 10 deletions.
diff --git a/vpipe.snake b/vpipe.snake
@@ -15,6 +15,7 @@ LOGGER = logging.getLogger('snakemake.logging')
 VPIPE_DEBUG = True if os.environ.get('VPIPE_DEBUG') is not None else False
 VPIPE_BENCH = True if os.environ.get('VPIPE_BENCH') is not None else False
 
+vpipe_basedir = workflow.basedir
 
 class VpipeConfig(object):
     'Class used to encapsulate the configuration properties used by V-pipe'
@@ -99,7 +100,7 @@ class VpipeConfig(object):
             'conda': __RECORD__(value='', type=str),
         }),
         ('create_vicuna_initial', {
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
         }),
         ('hmm_align', {
             'mem': __RECORD__(value=1250, type=int),
@@ -123,7 +124,7 @@ class VpipeConfig(object):
         ('coverage_QA', {
             'mem': __RECORD__(value=1250, type=int),
             'time': __RECORD__(value=235, type=int),
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
         }),
         ('msa', {
             'mem': __RECORD__(value=10000, type=int),
@@ -134,12 +135,12 @@ class VpipeConfig(object):
         ('convert_to_ref', {
             'mem': __RECORD__(value=8000, type=int),
             'time': __RECORD__(value=235, type=int),
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
         }),
         ('ref_bwa_index', {
             'mem': __RECORD__(value=2000, type=int),
             'time': __RECORD__(value=235, type=int),
-            'conda': __RECORD__(value='envs/bwa_align.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/bwa_align.yaml', type=str),
         }),
         ('bwa_align', {
             'mem': __RECORD__(value=1250, type=int),
@@ -150,7 +151,7 @@ class VpipeConfig(object):
         ('ref_bowtie_index', {
             'mem': __RECORD__(value=2000, type=int),
             'time': __RECORD__(value=235, type=int),
-            'conda': __RECORD__(value='envs/bowtie_align.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/bowtie_align.yaml', type=str),
         }),
         ('bowtie_align', {
             'mem': __RECORD__(value=1250, type=int),
@@ -165,7 +166,7 @@ class VpipeConfig(object):
         ('consensus_sequences', {
             'mem': __RECORD__(value=1250, type=int),
             'time': __RECORD__(value=235, type=int),
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
 
             'min_coverage': __RECORD__(value=50, type=int),
             'qual_thrd': __RECORD__(value=15, type=int),
@@ -175,13 +176,13 @@ class VpipeConfig(object):
             'mem': __RECORD__(value=1000, type=int),
             'time': __RECORD__(value=235, type=int),
             'threads': __RECORD__(value=0, type=int),
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
         }),
         ('coverage_intervals', {
             'mem': __RECORD__(value=1000, type=int),
             'time': __RECORD__(value=60, type=int),
             'threads': __RECORD__(value=0, type=int),
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
 
             'overlap': __RECORD__(value=False, type=bool),
             'coverage': __RECORD__(value=50, type=int),
@@ -219,7 +220,7 @@ class VpipeConfig(object):
         ('haploclique_visualization', {
             'mem': __RECORD__(value=2000, type=int),
             'time': __RECORD__(value=235, type=int),
-            'conda': __RECORD__(value='envs/smallgenomeutilities.yaml', type=str),
+            'conda': __RECORD__(value=f'{vpipe_basedir}/envs/smallgenomeutilities.yaml', type=str),
 
             'region_start': __RECORD__(value=0, type=int),
             'region_end': __RECORD__(value=9719, type=int),
@@ -261,7 +262,7 @@ class VpipeConfig(object):
                         cur_value = defaults.value if defaults.value else self.__members[
                             'general']['threads']
                     elif value == 'conda':
-                        cur_value = "envs/{}.yaml".format(section) if len(
+                        cur_value = f'{vpipe_basedir}/envs/{section}.yaml' if len(
                             defaults.value) == 0 else defaults.value
                     else:
                         cur_value = defaults.value