start on singularity support (#844)

seq2science/envs/get_fastq.yaml

@@ -7,4 +7,5 @@ dependencies:
   - pkgs/main::pigz=2.4
   - bioconda::sra-tools=2.11.0
   - bioconda::parallel-fastq-dump=0.6.7
+  - conda-forge::flock=0.2.3
   - conda-forge::conda-ecosystem-user-package-isolation=1.0

seq2science/envs/khmer.yaml

@@ -6,4 +6,5 @@ channels:
 dependencies:
   - bioconda::khmer=2.0
   - conda-forge::jq=1.6
+  - bioconda::grep=3.4
   - conda-forge::conda-ecosystem-user-package-isolation=1.0

seq2science/envs/samtools.yaml

@@ -5,4 +5,5 @@ channels:
   - defaults
 dependencies:
   - bioconda::samtools=1.14
+  - conda-forge::perl=5.32.1
   - conda-forge::conda-ecosystem-user-package-isolation=1.0

seq2science/rules/configuration_generic.smk

@@ -1,6 +1,7 @@
 """
 all logic not related to any specific workflows should be here.
 """
+container: "docker://quay.io/biocontainers/seq2science:0.7.2--pypyhdfd78af_0"
 
 import os.path
 import pickle

seq2science/rules/get_fastq.smk

@@ -39,7 +39,7 @@ rule run2sra:
         do
             # acquire a lock
             (
-                flock --timeout 30 200 || continue
+                flock -w 30 200 || continue
                 sleep 2
             ) 200>{pysradb_cache_lock}
 
@@ -92,7 +92,7 @@ rule sra2fastq_SE:
 
         # acquire the lock
         (
-            flock --timeout 30 200 || exit 1
+            flock -w 30 200 || exit 1
             sleep 3
         ) 200>{pysradb_cache_lock}
 
@@ -133,7 +133,7 @@ rule sra2fastq_PE:
 
         # acquire the lock
         (
-            flock --timeout 30 200 || exit 1
+            flock -w 30 200 || exit 1
             sleep 3
         ) 200>{pysradb_cache_lock}
 

seq2science/scripts/atacshift.pl

@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 #
 # atacshift: Correct for tn5 bias by shifting reads on the positive strand +4 and reads 
 #            on the negative strand -5. The CIGAR string is the same length as the read