[med-svn] [Git][med-team/sift][master] 7 commits: Fix Homepage

Andreas Tille (@tille) gitlab at salsa.debian.org
Tue Oct 20 08:33:26 BST 2026 


Andreas Tille pushed to branch master at Debian Med / sift


Commits:
dca5fd75 by Andreas Tille at 2026-10-20T08:14:50+02:00
Fix Homepage

- - - - -
c3237050 by Andreas Tille at 2026-10-20T08:16:43+02:00
d/watch:

   - Version 5
   - Fix

- - - - -
fd5549f1 by Andreas Tille at 2026-10-20T08:29:50+02:00
Remove all binaries from source

- - - - -
d33f1576 by Andreas Tille at 2026-10-20T08:33:46+02:00
New upstream version 6.2.1+ds
- - - - -
685d0783 by Andreas Tille at 2026-10-20T08:33:47+02:00
Update upstream source from tag 'upstream/6.2.1+ds'

Update to upstream version '6.2.1+ds'
with Debian dir 1ceb2200bfde081a1c28ab5c5b493de7c108ccf7
- - - - -
b0904808 by Andreas Tille at 2026-10-20T08:36:33+02:00
Do not install prebuild binaries from bin/web Closes: #1150426

- - - - -
341493b0 by Andreas Tille at 2026-10-20T09:33:00+02:00
Remove now unneeded lintian-overrides

- - - - -


21 changed files:

- − .INSTALL.swp
- − bin/linux/choose_seqs_via_psiblastseedmedian
- − bin/linux/clump_output_alignedseq
- − bin/linux/consensus_to_seq
- − bin/linux/fastaseqs
- − bin/linux/info_on_seqs
- − bin/linux/psiblast_res_to_fasta_dbpairwise
- − bin/linux/seqs_from_psiblast_res
- − bin/web/allowed_subst_html
- − bin/web/process_alignment
- − bin/web/seqs_to_matrixweb
- − bin/web/seqs_to_msf
- − bin/web/seqs_to_msf_web
- − blimps/lib/libblimps.a
- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- − debian/source/lintian-overrides
- debian/watch
- − formatdb.log


Changes:

=====================================
.INSTALL.swp deleted
=====================================
Binary files a/.INSTALL.swp and /dev/null differ


=====================================
bin/linux/choose_seqs_via_psiblastseedmedian deleted
=====================================
Binary files a/bin/linux/choose_seqs_via_psiblastseedmedian and /dev/null differ


=====================================
bin/linux/clump_output_alignedseq deleted
=====================================
Binary files a/bin/linux/clump_output_alignedseq and /dev/null differ


=====================================
bin/linux/consensus_to_seq deleted
=====================================
Binary files a/bin/linux/consensus_to_seq and /dev/null differ


=====================================
bin/linux/fastaseqs deleted
=====================================
Binary files a/bin/linux/fastaseqs and /dev/null differ


=====================================
bin/linux/info_on_seqs deleted
=====================================
Binary files a/bin/linux/info_on_seqs and /dev/null differ


=====================================
bin/linux/psiblast_res_to_fasta_dbpairwise deleted
=====================================
Binary files a/bin/linux/psiblast_res_to_fasta_dbpairwise and /dev/null differ


=====================================
bin/linux/seqs_from_psiblast_res deleted
=====================================
Binary files a/bin/linux/seqs_from_psiblast_res and /dev/null differ


=====================================
bin/web/allowed_subst_html deleted
=====================================
Binary files a/bin/web/allowed_subst_html and /dev/null differ


=====================================
bin/web/process_alignment deleted
=====================================
Binary files a/bin/web/process_alignment and /dev/null differ


=====================================
bin/web/seqs_to_matrixweb deleted
=====================================
Binary files a/bin/web/seqs_to_matrixweb and /dev/null differ


=====================================
bin/web/seqs_to_msf deleted
=====================================
Binary files a/bin/web/seqs_to_msf and /dev/null differ


=====================================
bin/web/seqs_to_msf_web deleted
=====================================
Binary files a/bin/web/seqs_to_msf_web and /dev/null differ


=====================================
blimps/lib/libblimps.a deleted
=====================================
Binary files a/blimps/lib/libblimps.a and /dev/null differ


=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+sift (6.2.1+ds-1) UNRELEASED; urgency=medium
+
+  [ Andreas Tille ]
+  * Fix Homepage
+  * d/watch:
+     - Version 5
+     - Fix
+  * Remove all binaries from source
+  * Remove now unneeded lintian-overrides
+
+  [ Sebastien Bacher ]
+  * Do not install prebuild binaries from bin/web
+    Closes: #1150426
+
+ -- Andreas Tille <tille at debian.org>  Tue, 20 Oct 2026 08:14:38 +0200
+
 sift (6.2.1-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
 Standards-Version: 4.7.2
 Vcs-Browser: https://salsa.debian.org/med-team/sift
 Vcs-Git: https://salsa.debian.org/med-team/sift.git
-Homepage: https://sift.bii.a-star.edu.sg/
+Homepage: https://siftdna.org/
 
 Package: sift
 Architecture: any


=====================================
debian/copyright
=====================================
@@ -7,16 +7,22 @@ Disclaimer: This package is not part of Debian because of the non-free
  FHCRC NONCOMMERCIAL LICENSE license.  The license does not restrict
  auto-building of the package.   Distribution on a royalty-free basis
  is allowed, therefore Debian is allowed to distribute the program.
-Files-Excluded: bin/choose_seqs_via_psiblastseedmedian
-                bin/clump_output_alignedseq
-                bin/consensus_to_seq
-                bin/fastaseqs
-                bin/info_on_seqs
-                bin/process_alignment
+Files-Excluded: bin/linux/c*
+                bin/linux/f*
+                bin/linux/i*
+                bin/linux/p*
+                bin/linux/s*
+                bin/web
+                bin/c*
+                bin/i*
                 bin/psiblast_res_to_fasta_dbpairwise
                 bin/seqs_from_psiblast_res
+                bin/web
+                blimps/lib
                 blimps/obj/*.o
-
+                tmp
+                .INSTALL.swp
+                formatdb.log
 
 Files: *
 Copyright: 1993-2008, Fred Hutchinson Cancer Research Center


=====================================
debian/rules
=====================================
@@ -61,7 +61,8 @@ override_dh_auto_install:
 
 override_dh_install:
 	# lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it
-	dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
+	# bin/web contains prebuilt x86-64 binaries, not built from source here
+	dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris -Xbin/web bin $(prefix)/lib/sift/
 	#dh_install bin/IntersectFeatures.jar $(pkgdatadir)/
 	dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/
 


=====================================
debian/source/lintian-overrides deleted
=====================================
@@ -1,7 +0,0 @@
-sift source: source-ships-excluded-file bin/choose_seqs_via_psiblastseedmedian
-sift source: source-ships-excluded-file bin/clump_output_alignedseq
-sift source: source-ships-excluded-file bin/consensus_to_seq
-sift source: source-ships-excluded-file bin/info_on_seqs
-sift source: source-ships-excluded-file bin/psiblast_res_to_fasta_dbpairwise
-sift source: source-ships-excluded-file bin/seqs_from_psiblast_res
-


=====================================
debian/watch
=====================================
@@ -1,3 +1,6 @@
-version=4
+Version: 5
 
-http://sift.bii.a-star.edu.sg/www/code.html .*/sift at ANY_VERSION@@ARCHIVE_EXT@
+Source: https://siftdna.org/www/code.html
+Matching-Pattern: .*/@PACKAGE@@ANY_VERSION@@ARCHIVE_EXT@
+Repack-Suffix: +ds
+Dversion-Mangle: auto


=====================================
formatdb.log deleted
=====================================
@@ -1,24 +0,0 @@
-
-========================[ Dec 5, 2016 11:13 AM ]========================
-Version 2.2.24 [Aug-08-2010]
-Started database file "/usr/local/web/packages2//tmp/lacI.TEMP_DB"
-Formatted 89 sequences in volume 0
-SUCCESS: formatted database /usr/local/web/packages2//tmp/lacI.TEMP_DB
-
-========================[ Dec 5, 2016 11:13 AM ]========================
-Version 2.2.24 [Aug-08-2010]
-Started database file "/usr/local/web/packages2//tmp/lacI.TEMP_DB"
-Formatted 84 sequences in volume 0
-SUCCESS: formatted database /usr/local/web/packages2//tmp/lacI.TEMP_DB
-
-========================[ Dec 5, 2016 11:13 AM ]========================
-Version 2.2.24 [Aug-08-2010]
-Started database file "/usr/local/web/packages2//tmp/lacI.TEMP_DB"
-Formatted 79 sequences in volume 0
-SUCCESS: formatted database /usr/local/web/packages2//tmp/lacI.TEMP_DB
-
-========================[ Dec 5, 2016 11:13 AM ]========================
-Version 2.2.24 [Aug-08-2010]
-Started database file "/usr/local/web/packages2//tmp/lacI.TEMP_DB"
-Formatted 74 sequences in volume 0
-SUCCESS: formatted database /usr/local/web/packages2//tmp/lacI.TEMP_DB



View it on GitLab: https://salsa.debian.org/med-team/sift/-/compare/c8dca91ae8df993e151dfce502bf08a17256a0cc...341493b054757efb682718c9f9f8c43c0e483e61

-- 
View it on GitLab: https://salsa.debian.org/med-team/sift/-/compare/c8dca91ae8df993e151dfce502bf08a17256a0cc...341493b054757efb682718c9f9f8c43c0e483e61
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