diff --git a/debian/changelog b/debian/changelog index ed6307d..2b94c1b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,7 @@ [ Sascha Steinbiss ] * Add patch to fix test failures. Closes: #963332 + * Add patch to call SPAdes correctly. -- Sascha Steinbiss Tue, 30 Jun 2020 12:32:39 +0200 diff --git a/debian/patches/run-debian-spades-wrapper.patch b/debian/patches/run-debian-spades-wrapper.patch new file mode 100644 index 0000000..7ad91f9 --- /dev/null +++ b/debian/patches/run-debian-spades-wrapper.patch @@ -0,0 +1,19 @@ +Description: run Debian SPAdes wrapper + Debian's /usr/bin/spades.py is not a Python script, but a wrapper + around a common executable only provided for compatibility reasons. + Ariba is trying to execute it explicitly as a Python script. + This patch just calls the executable without forcing it through the + Python interpreter. +Author: Sascha Steinbiss +Last-Update: 2020-06-30 +--- a/ariba/assembly.py ++++ b/ariba/assembly.py +@@ -140,7 +140,7 @@ + spades_out_seq_base = "contigs.fasta" + else: + raise ValueError("Unknown spades_mode value: {}".format(self.spades_mode)) +- asm_cmd = ['python3', spades_exe, "-t", str(self.threads), "--pe1-1", self.reads1, "--pe1-2", self.reads2, "-o", self.assembler_dir] + \ ++ asm_cmd = [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: diff --git a/debian/patches/series b/debian/patches/series index 4bdfe63..3f704c1 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -3,3 +3,4 @@ add-testdata.patch disable-tests-with-internet-access.patch support-pymummer-0.11.patch +run-debian-spades-wrapper.patch