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Bump version to 2.13.5 and fix Spades invocation issue #259

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merged 3 commits into from
Mar 26, 2019
Merged

Bump version to 2.13.5 and fix Spades invocation issue #259

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d78445d
Merge pull request #1 from sanger-pathogens/master
kpepper Mar 21, 2019
5b38230
Version number bump and updated CHANGELOG
kpepper Mar 22, 2019
54860e2
Modified Spades invocation to force running with Python 3 (fix for Sa…
kpepper Mar 26, 2019
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17 changes: 16 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -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:**
Expand All @@ -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)
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion ariba/assembly.py
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Expand Up @@ -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:
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11 changes: 8 additions & 3 deletions ariba/external_progs.py
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -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/*']},
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