[med-svn] [Git][med-team/umis][master] 6 commits: d/copyright
Andreas Tille
gitlab at salsa.debian.org
Sat Apr 13 07:58:18 BST 2019
Andreas Tille pushed to branch master at Debian Med / umis
Commits:
7087b8c5 by Andreas Tille at 2019-04-13T05:54:30Z
d/copyright
- - - - -
c3b5d1aa by Andreas Tille at 2019-04-13T06:01:38Z
Add tests and examples to separate package
- - - - -
0d76cc18 by Andreas Tille at 2019-04-13T06:07:58Z
Provide autopkgtest
- - - - -
414a3248 by Andreas Tille at 2019-04-13T06:20:51Z
Add citation
- - - - -
114880e4 by Andreas Tille at 2019-04-13T06:57:26Z
Add dependencies
- - - - -
21bae217 by Andreas Tille at 2019-04-13T06:57:38Z
Install to /usr/share/doc/umis
- - - - -
10 changed files:
- debian/README.test
- debian/control
- debian/copyright
- − debian/lintian-overrides
- + debian/patches/fix_bashism.patch
- + debian/patches/series
- debian/tests/run-unit-test
- + debian/umis-examples.install
- + debian/umis.docs
- debian/upstream/metadata
Changes:
=====================================
debian/README.test
=====================================
@@ -1,7 +1,8 @@
Notes on how this package can be tested.
────────────────────────────────────────
-This package can be tested by running the provided test:
+This package can be tested by running the provided test which can be
+found in the package umis-examples:
sh run-unit-test
=====================================
debian/control
=====================================
@@ -17,7 +17,14 @@ Package: umis
Architecture: any
Depends: ${shlibs:Depends},
${python3:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ python3-click,
+ python3-pysam,
+ python3-pandas,
+ python3-regex,
+ python3-scipy,
+ python3-toolz
+Suggests: umis-examples
Description: tools for processing UMI RNA-tag data
Umis provides tools for estimating expression in RNA-Seq data which
performs sequencing of end tags of transcript, and incorporate molecular
@@ -29,3 +36,22 @@ Description: tools for processing UMI RNA-tag data
2. Filtering noisy cellular barcodes
3. Pseudo-mapping to cDNAs
4. Counting molecular identifiers
+
+Package: umis-examples
+Architecture: all
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+Recommends: umis
+Description: tools for processing UMI RNA-tag data (examples)
+ Umis provides tools for estimating expression in RNA-Seq data which
+ performs sequencing of end tags of transcript, and incorporate molecular
+ tags to correct for amplification bias.
+ .
+ There are four steps in this process.
+ .
+ 1. Formatting reads
+ 2. Filtering noisy cellular barcodes
+ 3. Pseudo-mapping to cDNAs
+ 4. Counting molecular identifiers
+ .
+ Example and test files for umis.
=====================================
debian/copyright
=====================================
@@ -1,16 +1,30 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: umis
-Source: <path_to_download>
-Comment: **** Before manually editing this file you should give ****
- scan-copyrights
- **** available in cme + lib-config-model-dpkg-perl ****
- **** package a try. For existing copyright files try ****
- cme update dpkg-copyright
+Source: https://github.com/vals/umis
Files: *
-Copyright: 20xx-20yy <upstream>
-License: <license>
+Copyright: 2016 Valentine Svensson
+License: MIT
Files: debian/*
Copyright: 2019 Andreas Tille <tille at debian.org>
-License: <license>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in all
+ copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
=====================================
debian/lintian-overrides deleted
=====================================
@@ -1,2 +0,0 @@
-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-#PKGNAME#: script-with-language-extension usr/bin/*.*
=====================================
debian/patches/fix_bashism.patch
=====================================
@@ -0,0 +1,21 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 13 Apr 2019 07:12:50 +0200
+Description: Fix bashism in test script
+
+--- a/test.sh
++++ b/test.sh
+@@ -1,3 +1,5 @@
++#!/bin/sh
++
+ rm -r tests/results
+ mkdir -p tests/results
+
+@@ -192,7 +194,7 @@ examples/Klein-inDrop/test_cell_demultip
+
+
+ # only display diff output if there are differences
+-if [[ $(diff -rq tests/results tests/correct) ]]; then
++if [ $(diff -rq tests/results tests/correct) ] ; then
+ diff -rq tests/results tests/correct
+ exit 1
+ else
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+fix_bashism.patch
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
#!/bin/bash
set -e
-pkg=#PACKAGENAME#
+pkg=umis
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -11,8 +11,10 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+cp -a /usr/share/doc/${pkg}/test* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
-#do_stuff_to_test_package#
+gunzip -r *
+
+sh test.sh
=====================================
debian/umis-examples.install
=====================================
@@ -0,0 +1,4 @@
+examples usr/share/doc/umis
+tests usr/share/doc/umis
+test.sh usr/share/doc/umis
+debian/tests/run-unit-test usr/share/doc/umis
=====================================
debian/umis.docs
=====================================
@@ -0,0 +1 @@
+debian/README.test
=====================================
debian/upstream/metadata
=====================================
@@ -1,12 +1,11 @@
Reference:
- Author:
- Title:
- Journal:
- Year:
- Volume:
+ Author: Valentine Svensson and Kedar Nath Natarajan and Lam-Ha Ly and Ricardo J Miragaia and Charlotte Labalette and Iain C Macaulay and Ana Cvejic and Sarah A Teichmann
+ Title: "Power analysis of single-cell RNA-sequencing experiments"
+ Journal: Nature methods
+ Year: 2017
+ Volume: 14
Number:
- Pages:
- DOI:
- PMID:
- URL:
- eprint:
+ Pages: 381–387
+ DOI: 10.1038/nmeth.4220
+ PMID: 28263961
+ URL: https://www.nature.com/articles/nmeth.4220
View it on GitLab: https://salsa.debian.org/med-team/umis/compare/3b39c3dc1810bd6950bfb34d2826bd7202325134...21bae217affcdf00f12f69d9b38023f0c88b9ffb
--
View it on GitLab: https://salsa.debian.org/med-team/umis/compare/3b39c3dc1810bd6950bfb34d2826bd7202325134...21bae217affcdf00f12f69d9b38023f0c88b9ffb
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