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 <[email protected]> Sun, 24 May 2020 06:37:36 +0200 ===================================== debian/control ===================================== @@ -3,10 +3,12 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> 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 <[email protected]> +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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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