[med-svn] [Git][med-team/ensembl-vep][master] Add todo

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / ensembl-vep


Commits:
4b1f2bae by Andreas Tille at 2020-05-28T11:36:04+02:00
Add todo

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/install
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,10 @@
 ensembl-vep (100.2-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
+  TODO:
+     1. Can't locate Bio/EnsEMBL/Registry.pm in @INC (you may need to install the Bio::EnsEMBL::Registry module)
+        ---> https://plants.ensembl.org/info/docs/api/registry.html
+     2. Check install method - probably there is some more elegant way than debian/install
+     3. Run Build time tests
 
  -- Andreas Tille <tille at debian.org>  Thu, 28 May 2020 09:22:57 +0200


=====================================
debian/control
=====================================
@@ -3,7 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 13)
+Build-Depends: debhelper-compat (= 13),
+               libmodule-build-perl,
+               perl
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/ensembl-vep
 Vcs-Git: https://salsa.debian.org/med-team/ensembl-vep.git
@@ -12,7 +14,15 @@ Homepage: https://github.com/Ensembl/ensembl-vep/
 Package: ensembl-vep
 Architecture: any
 Depends: ${perl:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         libarchive-zip-perl,
+         libdbi-perl
+Recommends: libdbd-mariadb-perl,
+            libset-intervaltree-perl,
+            libjson-perl,
+            libperlio-gzip-perl,
+Suggests: libbio-db-bigfile-perl
+# Bio::DB::BigFile is not yet packaged: https://metacpan.org/pod/release/LDS/Bio-BigFile-1.07/lib/Bio/DB/BigFile.pm
 Description: Variant Effect Predictor predicting the functional effects of genomic variants
  The Ensembl Variant Effect Predictor predicts the functional effects of
  genomic variants. It has three components:


=====================================
debian/install
=====================================
@@ -0,0 +1,5 @@
+filter_vep	usr/bin
+haplo		usr/bin
+variant_recoder	usr/bin
+vep		usr/bin
+modules/*	usr/share/perl5


=====================================
debian/rules
=====================================
@@ -20,6 +20,12 @@ include /usr/share/dpkg/default.mk
 %:
 	dh $@
 
+override_dh_install:
+	dh_install
+	for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` ; do \
+	    sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \
+	done
+
 ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
 #override_dh_auto_test:
 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))



View it on GitLab: https://salsa.debian.org/med-team/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c

-- 
View it on GitLab: https://salsa.debian.org/med-team/ensembl-vep/-/commit/4b1f2bae85fca248e5c4c7f3a1dba2d02faeff7c
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