Package: cct / 1:1.0.0-1

Metadata

Package Version Patches format
cct 1:1.0.0-1 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
cgview_path.patch | (download)

conf/global_settings.conf | 2 1 + 1 - 0 !
scripts/create_zoomed_maps.sh | 2 1 + 1 - 0 !
scripts/redraw_maps.sh | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 make sure test will work and set correct path to cgview.jar


testscripts.patch | (download)

lib/scripts/assign_cogs/test.sh | 2 1 + 1 - 0 !
scripts/build_cog_db.sh | 21 11 + 10 - 0 !
scripts/process_test_projects.sh | 11 6 + 5 - 0 !
3 files changed, 18 insertions(+), 16 deletions(-)

 fix some test scripts regarding paths and robustness regarding download (s/ftp:/http:/)


fix_cgview_path.patch | (download)

lib/scripts/cgview_xml_builder/test.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix path to cgview.jar in test script


conditionalize_blast_ Q_ D.patch | (download)

lib/scripts/local_blast_client/local_blast_client.pl | 11 10 + 1 - 0 !
1 file changed, 10 insertions(+), 1 deletion(-)

 address blast usage errors as of blast+ 2.10.

Supply the legacy blastall command's -Q and -D flags only in BLAST
variants that involve translating queries and subjects respectively.
(tblastx notably translates both.)

NB: The use of -v $settings{HITLIST_SIZE} in conjunction with the
supplied $format_type value (7 or 9) results in the warning

    Warning: [tblastn] The parameter -num_descriptions is ignored for output formats > 4 . Use -max_target_seqs to control output

Actually substituting -max_target_seqs would require bypassing the
legacy blastall wrapper, which isn't entirely straightforward in this
instance due to the need to convert a variable format string to modern
options.  (Also, this script technically only knows the path to
blastall, though that shouldn't be a concern in practice on Debian.)