Bugzilla Bug 123332

I would like all supporting arches to please stabilise 
sci-biology/emboss-3.0.0-r1. This will require stabilising
sci-biology/rebase-601-r1. To test EMBOSS, use:

$ wget pelican.rsvs.ulaval.ca/distfiles/seq/emboss-test.sh
$ chmod + x emboss-test.sh
$ ./emboss-test.sh

This script will download a sequence from a server, do some manipulations, and
finally compare the results with reference files. If the tests are sucessful
(ie. the only differences shown are timestamps), the package is ready to be
stabilised on your arch. (See the comments in the file for more details.)

To test Rebase, use:

$ wget pelican.rsvs.ulaval.ca/distfiles/seq/phikz-orf144.fasta  
$ wget pelican.rsvs.ulaval.ca/distfiles/seq/phikz-orf144-ref.restrict  
$ restrict -enzymes all -sitelen 4 phikz-orf144.fasta stdout | grep -v '#' | 
sort > phikz-orf144.restrict
$ diff -u phikz-orf144-ref.restrict phikz-orf144.restrict

If there are no differences, the package should be stabilised on your arch.

Thanks in advance,

Created an attachment (id=80194) [details]
diff on ppc64

Hi,

there is a difference on PPC64, when running the last command (diff -u
phikz-orf144-ref.restrict phikz-orf144.restrict).

What can I do?

doing a closer look it seems like the lines were just swaped. Unfortunaly I
don't know if this makes a difference or not...

Same results here on x86. Please advise

Swaped entries are not a problem. (Although I wonder why we still have them now
that the reference file and the restrict output are sorted.)

Stable on x86

stable on ppc64

Stable on ppc

emboss ok (including diffs), ppc-macos stable
rebase ok (swapped lines), ppc-macos stable


PS, your emboss-test.sh script lacks a 'j' in its tar command, that's why it
doesn't run on OSX.

amd64, could you have a look at this please? (Last arch to stabilise.)

Can't mark emboss 3.0.0-r1 stable on amd64. Following the output of diff:

dvandyk@phi gentoo $ diff -u phikz-orf144-ref.restrict phikz-orf144.restrict
--- phikz-orf144-ref.restrict   2006-03-15 13:16:05.000000000 +0100
+++ phikz-orf144.restrict       2006-03-15 13:12:52.000000000 +0100
@@ -68,11 +68,11 @@
     369     372 AluI        AGCT                370    370         .         .
     369     372 CviJI       RGCY                370    370         .         .
     371     375 DdeI        CTNAG               371    374         .         .
+    380     385 PstII       CATCAG              410    412         .         .
     382     378 TspDTI      ATGAA               368    366         .         .
     383     391 AlwNI       CAGNNNCTG           388    385         .         .
     384     387 AluI        AGCT                385    385         .         .
     384     387 CviJI       RGCY                385    385         .         .
-    385     380 PstII       CTGATG              352    354         .         .
     388     392 BsrI        ACTGG               393    391         .         .
     395     400 NlaIV       GGNNCC              397    397         .         .
     399     413 XcmI        CCANNNNNNNNNTGG     406    405         .         .

Please advise.

(In reply to comment #10)
> Can't mark emboss 3.0.0-r1 stable on amd64. Following the output of diff:

If that is the only diff, you can mark it stable. This is a case where the
restriction site was found correctly but on the reverse complement sequence
(ie. 380-385 becomes 385-380, and CATCAG becomes CTGATG by reversing and
swaping A/T and C/G).

amd64 team, can you look at this, please? (See comment 11).

we're finally done here, sorry for the delay