Merge pull request #259 from kpepper/bump_version_to_2.13.5

Bump version to 2.13.5 and fix Spades invocation issue

CHANGELOG.md

@@ -1,6 +1,20 @@
 # Change Log
 
-## [v2.13.4](https://github.com/sanger-pathogens/ariba/tree/v2.13.3) (2019-03-15)
+## [v2.13.5](https://github.com/sanger-pathogens/ariba/tree/v2.13.5) (2019-03-22)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.4...v2.13.5)
+
+**Closed issues:**
+
+- Installation failed: clang: error: linker command failed with exit code 1 \(use -v to see invocation\) [\#245](https://github.com/sanger-pathogens/ariba/issues/245)
+- virfinddb db not downloading properly [\#229](https://github.com/sanger-pathogens/ariba/issues/229)
+- getref error with resfinder db [\#225](https://github.com/sanger-pathogens/ariba/issues/225)
+- Ariba fails without --noclean depending on database [\#205](https://github.com/sanger-pathogens/ariba/issues/205)
+
+**Merged pull requests:**
+
+- Minor code change to mitigate issue \#245 \(installation failure\) [\#258](https://github.com/sanger-pathogens/ariba/pull/258) ([kpepper](https://github.com/kpepper))
+
+## [v2.13.4](https://github.com/sanger-pathogens/ariba/tree/v2.13.4) (2019-03-15)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.3...v2.13.4)
 
 **Closed issues:**
@@ -10,6 +24,7 @@
 
 **Merged pull requests:**
 
+- Rebuilt CHANGELOG for v2.13.4 [\#257](https://github.com/sanger-pathogens/ariba/pull/257) ([kpepper](https://github.com/kpepper))
 - Allow increasing cd-hit-est memory allocation \#255 [\#256](https://github.com/sanger-pathogens/ariba/pull/256) ([kpepper](https://github.com/kpepper))
 
 ## [v2.13.3](https://github.com/sanger-pathogens/ariba/tree/v2.13.3) (2019-01-02)

Dockerfile

@@ -31,7 +31,7 @@ RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd
 
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
-  && git checkout v2.13.4 \
+  && git checkout v2.13.5 \
   && python3 setup.py test \
   && python3 setup.py install
 

ariba/assembly.py

@@ -140,7 +140,7 @@ def _assemble_with_spades(self):
                 spades_out_seq_base = "contigs.fasta"
             else:
                 raise ValueError("Unknown spades_mode value: {}".format(self.spades_mode))
-            asm_cmd = [spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \
+            asm_cmd = ['python3', spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \
                 spades_options
             asm_ok,err = common.syscall(asm_cmd, verbose=True, verbose_filehandle=self.log_fh, shell=False, allow_fail=True)
             if not asm_ok:

ariba/external_progs.py

@@ -144,9 +144,14 @@ def _get_version(prog, path):
            Returns tuple (bool, version). First element True iff found version ok.
            Second element is version string (if found), otherwise an error message'''
         assert prog in prog_to_version_cmd
-        cmd, regex = prog_to_version_cmd[prog]
-        cmd = path + ' ' + cmd
-        cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+        args, regex = prog_to_version_cmd[prog]
+        cmd = path + ' ' + args
+        if prog == 'spades':
+            cmd_output = subprocess.Popen(['python3', path, args], shell=False, stdout=subprocess.PIPE,
+                                          stderr=subprocess.PIPE).communicate()
+        else:
+            cmd_output = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
+
         cmd_output = common.decode(cmd_output[0]).split('\n')[:-1] + common.decode(cmd_output[1]).split('\n')[:-1]
 
         for line in cmd_output:

setup.py

@@ -55,7 +55,7 @@
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.13.4',
+    version='2.13.5',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},