[med-svn] [Git][med-team/sepp][master] Proceed with pplacer available now

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / sepp


Commits:
6e143e1e by Andreas Tille at 2020-07-22T21:58:28+02:00
Proceed with pplacer available now

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- debian/patches/setup.patch
- + debian/patches/use_debian_packaged_guppy_from_pplacer.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,6 +1,5 @@
 sepp (4.3.10+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
-    Needs https://salsa.debian.org/med-team/pplacer
 
  -- Andreas Tille <tille at debian.org>  Sun, 24 May 2020 06:37:36 +0200


=====================================
debian/control
=====================================
@@ -3,10 +3,12 @@ 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 (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3,
-               python3-setuptools
+               python3-setuptools,
+               pplacer,
+               hmmer
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/sepp
 Vcs-Git: https://salsa.debian.org/med-team/sepp.git


=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
 setup.patch
+use_debian_packaged_guppy_from_pplacer.patch


=====================================
debian/patches/setup.patch
=====================================
@@ -1,3 +1,8 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2020-05-24 15:54:37 +0200
+Description: Do not check existence of third party tools since these are
+ removed.  We are using Debian packaged tools
+
 --- a/setup.py
 +++ b/setup.py
 @@ -38,9 +38,9 @@ def get_tools_dir(where):


=====================================
debian/patches/use_debian_packaged_guppy_from_pplacer.patch
=====================================
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 22 Jul 2020 21:53:32 +0200
+Description: Use Debian packaged guppy
+
+--- a/sepp-package/run-sepp.sh
++++ b/sepp-package/run-sepp.sh
+@@ -146,7 +146,7 @@ cp $tmp/${name}_rename-json.py .
+ # we might want to split computation in two parts: a) obtaining placements and b) creation of an insertion tree.
+ # If -n set to something, we stop after a) and leave it to the user to compute b) afterwards.
+ if [ -z ${noTree+x} ]; then
+-	gbin=$( dirname `grep -A1 "pplacer" $DIR/sepp/.sepp/main.config |grep path|sed -e "s/^path=//g"` )
++	gbin="/usr/bin/"
+ 
+ 	$gbin/guppy tog ${name}_placement.json
+ 
+--- a/setup.py
++++ b/setup.py
+@@ -45,7 +45,7 @@ def get_tools_dir(where):
+ 
+ 
+ def get_tool_name(tool, bits):
+-    if platform.system() == "Darwin" or not bits:  # MAC doesn't have 32/64
++    if platform.system() == "Darwin" or True:  # Never add anything to tool name under Debian
+         return tool
+     is_64bits = sys.maxsize > 2**32
+     return "%s-%s" % (tool, "64" if is_64bits else "32")
+@@ -81,7 +81,7 @@ class ConfigSepp(Command):
+ 
+     def copy_tool_to_lib(self, tool, where=None, bits=True):
+         shutil.copy2(
+-            os.path.join(get_tools_dir(where), get_tool_name(tool, bits)),
++            os.path.join("/usr/bin", get_tool_name(tool, bits)),
+             os.path.join(self.get_tools_dest(), tool))
+ 
+     def initialize_options(self):



View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b

-- 
View it on GitLab: https://salsa.debian.org/med-team/sepp/-/commit/6e143e1e7abc420c81418e63400c7f2679e62e9b
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