fixes for snap

Author: dmnfarrell

setup.py

@@ -9,7 +9,8 @@
                     'pysam>=0.10.0',
                     'HTSeq>=0.6',
                     'bx-python>=0.5',
-                    'forgi==0.20']
+                    'forgi==1.1',
+                    'logging_exceptions']
 
 major, minor, micro = sys.version_info[:3]
 if major == '2':

smallrnaseq/aligners.py

@@ -49,18 +49,23 @@ def set_params(aligner, params=None):
         global SUBREAD_PARAMS
         SUBREAD_PARAMS = params
 
-def build_bowtie_index(fastafile, path):
-    """Build a bowtie index"""
+def build_bowtie_index(fastafile, path=None):
+    """Build a bowtie index
+    Args:
+        fastafile: file input
+        path: folder to place index files
+    """
 
-    name = os.path.splitext(fastafile)[0]
+    name = os.path.splitext(os.path.basename(fastafile))[0]
+    name = os.path.join(path, name)
+    if not os.path.exists(path):
+        os.makedirs(path)
     cmd = 'bowtie-build -f %s %s' %(fastafile, name)
     try:
         result = subprocess.check_output(cmd, shell=True, executable='/bin/bash')
     except subprocess.CalledProcessError as e:
         print (str(e.output))
         return
-    files = glob.glob(name+'*.ebwt')
-    utils.move_files(files, path)
     print ('built bowtie index for %s' %fastafile)
     return
 
@@ -120,4 +125,4 @@ def subread_align(infile, ref, outfile):
     print (cmd)
     result = subprocess.check_output(cmd, shell=True, executable='/bin/bash',
                                      stderr= subprocess.STDOUT)
-    return
+    return

smallrnaseq/app.py

@@ -23,6 +23,8 @@
 import glob
 import pandas as pd
 from smallrnaseq import config, base, analysis, utils, aligners, novel, plotting, de
+snap_msg = 'when running from a snap you should use your home folder for reading/writing'
+home = os.path.expanduser('~')
 
 class WorkFlow(object):
     """Class for implementing a rna/mirna workflow from a set of options"""
@@ -43,16 +45,22 @@ def setup(self):
             self.files = glob.glob(os.path.join(self.path,'*.fastq'))
             if len(self.files) == 0:
                 print ('no fastq files found')
+                if check_snap() == True:
+                    print (snap_msg)
                 return False
         else:
             print ('you should provide at least one file or folder')
+            if check_snap() == True:
+                print (snap_msg)
             return False
         self.files = [str(f) for f in self.files]
         aligners.BOWTIE_INDEXES = aligners.SUBREAD_INDEXES = self.index_path
         if self.default_params != '':
             aligners.set_params(self.aligner, self.default_params)
         if not os.path.exists(self.index_path):
             print ('no such folder for indexes')
+            if check_snap() == True:
+                print (snap_msg)
             return False
         if not os.path.exists(self.output):
             os.mkdir(self.output)
@@ -189,7 +197,7 @@ def map_mirnas(self):
         #novel prediction
         if self.ref_fasta == '' or not os.path.exists(self.ref_fasta):
             print ('no reference genome file, skipping novel mirna step')
-        elif ref_name == None:
+        elif ref_name == None or ref_name == '':
             print ('no index for ref genome, required for novel mirna step')
         elif check_viennarna() == False:
             print ('Vienna RNA package not installed')
@@ -413,16 +421,23 @@ def print_help():
     print ('for further information')
     return
 
-def run_test():
+def check_snap():
+    """Check if inside a snap"""
+
+    if 'SNAP_COMMON' in os.environ:
+        return True
+    return False
+
+def test_run():
     """Run mirna test with test files"""
 
     print ('running miRNA counting test')
-    indpath = 'testing/indexes'
-    aligners.BOWTIE_INDEXES = indpath
-    if not os.path.exists(indpath):
-        os.makedirs(indpath)
+    idxpath = 'testing/indexes'
+    if check_snap() == True:
+        idxpath = os.path.join(home, idxpath)
+    aligners.BOWTIE_INDEXES = idxpath
     lib1 = os.path.join(base.datadir, 'bosTau8-tRNAs.fa')
-    aligners.build_bowtie_index(lib1, path=indpath)
+    aligners.build_bowtie_index(lib1, path=idxpath)
     f1 = os.path.join(base.datadir, 'bovine_plasma_sample.fastq')
     f2 = os.path.join(base.datadir, 'bovine_serum_sample.fastq')
     path = os.path.join('testing', 'ncrna_map')
@@ -463,7 +478,11 @@ def main():
         if opts.collapse == True:
             base.collapse_reads(opts.infile)
     elif opts.build != None:
-        build_indexes(opts.build, 'indexes')
+        idxpath = 'indexes'
+        if check_snap() == True:
+            idxpath = os.path.join(home, 'indexes')
+        build_indexes(opts.build, idxpath)
+        print ('wrote index to folder %s' %idxpath)
     elif opts.config != None and os.path.exists(opts.config):
         cp = config.parse_config(opts.config)
         options = config.get_options(cp)
@@ -484,7 +503,7 @@ def main():
         else:
             print_help()
     elif opts.tests == True:
-        run_test()
+        test_run()
     else:
         if opts.config != None:
             conffile = opts.config

smallrnaseq/base.py

@@ -40,7 +40,6 @@
 datadir = os.path.join(path, 'data')
 MIRBASE = os.path.join(datadir, 'miRBase_all.csv')
 
-
 def first(x):
     return x.iloc[0]
 

smallrnaseq/utils.py

@@ -539,6 +539,7 @@ def combine_aligned_reads(path, idx, filenames=None):
         #print(f)
         name = os.path.splitext(os.path.basename(f))[0]
         samfile = os.path.join(path, '%s_%s.sam' %(name,idx))
+        #print (samfile)
         if not os.path.exists(samfile):
             print ('no sam file')
             continue
@@ -716,7 +717,7 @@ def get_bg(seq, struct=None):
     bg.from_dotbracket(struct)
     #print (bg.struct)
     try:
-        bg.seq = seq        
+        bg.seq = seq
         return bg
     except Exception as e:
         print (e)

snap/snapcraft.yaml

@@ -14,24 +14,22 @@ icon: gui/icon.png
 apps:
   smallrnaseq:
     command: bin/smallrnaseq
-    plugs: [home,x11,network-bind]
+    plugs: [home,network-bind]
 parts:
   part1:
     #required for bx-python to build
     plugin: python
     python-version: python3
     python-packages:
       [numpy]
-    stage-packages:
-      [libblas3,libopenblas-dev]
   smallrnaseq:
     plugin: python
     python-version: python3
     source: ../
     python-packages:
-      [Cython,scipy,matplotlib]
+      [scipy,matplotlib]
     build-packages:
       [zlib1g-dev,liblzo2-dev]
     stage-packages:
-      [swig3.0,bowtie,ncbi-blast+,samtools,vienna-rna]
+      [bowtie,ncbi-blast+,samtools,vienna-rna,python3-rna]
     after: [part1]