[med-svn] [Git][med-team/ncbi-igblast][master] 5 commits: Link in internal_data/ directory locally for autopkgtest, as it does not get...

[Andrius Merkys (@merkys)]

Andrius Merkys pushed to branch master at Debian Med / ncbi-igblast


Commits:
ed67e3dc by Andrius Merkys at 2025-03-06T03:39:59-05:00
Link in internal_data/ directory locally for autopkgtest, as it does not get automatically detected on some hosts.

- - - - -
d3423ed0 by Andrius Merkys at 2025-03-07T02:20:09-05:00
Use chrpath to remove RUNPATH from binaries.

- - - - -
0ae12ba1 by Andrius Merkys at 2025-03-07T02:21:07-05:00
Sort B-Ds.

- - - - -
baa06a6d by Andrius Merkys at 2025-03-07T02:22:16-05:00
Build with system-provided mbedtls.

- - - - -
516b5f92 by Andrius Merkys at 2025-03-07T02:23:03-05:00
Update changelog for 1.20.0-2 release

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/rules
- debian/tests/igblast


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+ncbi-igblast (1.20.0-2) unstable; urgency=medium
+
+  * Link in internal_data/ directory locally for autopkgtest, as it does not
+    get automatically detected on some hosts.
+  * Use chrpath to remove RUNPATH from binaries.
+  * Build with system-provided mbedtls.
+
+ -- Andrius Merkys <merkys at debian.org>  Fri, 07 Mar 2025 02:22:46 -0500
+
 ncbi-igblast (1.20.0-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -5,10 +5,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: David Miguel Susano Pinto <carandraug+dev at gmail.com>,
            Steffen Moeller <moeller at debian.org>,
            Andrius Merkys <merkys at debian.org>
-Build-Depends: debhelper-compat (= 13),
-               time,
+Build-Depends: chrpath,
+               debhelper-compat (= 13),
+               libmbedtls-dev,
                libncbi-vdb-dev,
-               procps
+               procps,
+               time
 Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/ncbi-igblast
 Vcs-Git: https://salsa.debian.org/med-team/ncbi-igblast.git


=====================================
debian/rules
=====================================
@@ -14,6 +14,7 @@ VDB_INCLUDE=$(VDB_INC) $(VDB_SUBTREES:%=$(VDB_INC)/%)
 override_dh_auto_configure:
 	cd c++ && yes | \
         ./configure.orig --prefix=/usr \
+	  --with-mbedtls \
 	  --with-openmp $(WITH_OPTIM) \
 	  --with-vdb=/usr VDB_INCLUDE="$(VDB_INCLUDE)" \
 	  --without-runpath \
@@ -23,6 +24,7 @@ override_dh_auto_configure:
 
 override_dh_auto_build:
 	cd c++/*/build && make -f Makefile.flat app/igblast/
+	find . -name igblastn -o -name igblastp | xargs chrpath --delete
 
 override_dh_auto_install:
 	find . -name igblastn


=====================================
debian/tests/igblast
=====================================
@@ -7,6 +7,7 @@ cp c++/src/objtools/blast/seqdb_writer/unit_test/data/WP_009685663.fasta ${TMPDI
 
 (
     cd ${TMPDIR}
+    ln -s /usr/share/ncbi/igblast/internal_data
     igblastp -germline_db_V mouse_V -query WP_009685663.fasta
 )
 



View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/6fa8c3753ef168fd6a97e8b357e0e669c6f6643e...516b5f92f2e496bab5e4bde6f5e84623e37cfa1c

-- 
View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/6fa8c3753ef168fd6a97e8b357e0e669c6f6643e...516b5f92f2e496bab5e4bde6f5e84623e37cfa1c
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