Hi Andreas,
Fine with me if you would like to forward our conversation to the list.
The attached patch should fix the glitch with the dependencies of
bam_cigar_test.py you correctly identified.
Perhaps I should try and package smalt myself but I have no experience
with this and currently not much time.
Kind regards,
/Hannes
On 09/04/14 09:28, Andreas Tille wrote:
[Metaquestion: Usually we do all discussion in public on our
mailing list. Would you give me permission to forward our
conversation to the list?]
Hi again,
I made some step forward with the tests (see below)
On Tue, Apr 08, 2014 at 07:38:54PM +0200, Andreas Tille wrote:
ERROR when mapping: returned with code 1
FAIL: bam_cigar_test.py
=================================
1 of 7 tests failed
Please report to h...@sanger.ac.uk
=================================
According to the logfile this is related to the fact that bambamc
library is missing. While I plan to package bambamc library as well
(just contacted the author[1]) for now I builded the package with the
option --with-bambamc=no. Unfortunately this did not helped excluding
the test and I think the problem is in the test/Makefile.am which says:
if WITH_BAMBAMC
TESTS += ioform_test.py xali_test.py
endif
if WITH_SAMTOOLS_EXEC
TESTS += bam_cigar_test.py
endif
So bam_cigar_test.py is not excluded from the tests if bambamc is
missing. I tried some patch to Makefile.am (attached) but this fails
unfortunately. I have to admit I had to fight through strange automake
warnings telling me I should enable
AUTOMAKE_OPTIONS = subdir-objects
and to set
AM_PROG_AR
in the main Makefile.am. Perhaps these are some "features" of later
automake versions. Unfortunately I ended up with a Makefile which
contains a line
... am__expect_failure=no;; esac; /usr/bin/python /bin/bash ../test-driver
--test-name "$f"
which is totally stupid since python tries to call /bin/bash which for
sure ends up in a failure. I have no clue why automake might create
this nonsense and I think I'll leave it to you how to drop the
bam_cigar_test.py apropriately from the tests if bambamc is missing.
Kind regards
Andreas.
[1] https://lists.debian.org/debian-med/2014/04/msg00023.html
--
Hannes Ponstingl, Ph.D.
Sequence Assembly & Analysis Group Tel: +44 (0)1223 834244 x7345
The Wellcome Trust Sanger Institute Fax: +44 (0)1223 494919
Hinxton, Cambridge CB10 1SA, UK. E-mail: h...@sanger.ac.uk
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE. --- a/test/Makefile.am
+++ b/test/Makefile.am
@@ -89,11 +89,10 @@ TESTS += ${TEST_DRIVERS}
if WITH_BAMBAMC
TESTS += ioform_test.py xali_test.py
-endif
-
if WITH_SAMTOOLS_EXEC
TESTS += bam_cigar_test.py
endif
+endif
else
TESTS =
