add patch to call SPAdes correctly
Sascha Steinbiss
3 years ago
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[ Sascha Steinbiss ]
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* Add patch to fix test failures.
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Closes: #963332
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* Add patch to call SPAdes correctly.
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-- Sascha Steinbiss <satta@debian.org> Tue, 30 Jun 2020 12:32:39 +0200
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Description: run Debian SPAdes wrapper
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Debian's /usr/bin/spades.py is not a Python script, but a wrapper
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around a common executable only provided for compatibility reasons.
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Ariba is trying to execute it explicitly as a Python script.
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This patch just calls the executable without forcing it through the
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Python interpreter.
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Author: Sascha Steinbiss <satta@debian.org>
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Last-Update: 2020-06-30
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--- a/ariba/assembly.py
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+++ b/ariba/assembly.py
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@@ -140,7 +140,7 @@
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spades_out_seq_base = "contigs.fasta"
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else:
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raise ValueError("Unknown spades_mode value: {}".format(self.spades_mode))
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- asm_cmd = ['python3', spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \
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+ asm_cmd = [spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \
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spades_options
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asm_ok,err = common.syscall(asm_cmd, verbose=True, verbose_filehandle=self.log_fh, shell=False, allow_fail=True)
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if not asm_ok:
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add-testdata.patch
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disable-tests-with-internet-access.patch
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support-pymummer-0.11.patch
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run-debian-spades-wrapper.patch
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