debian/README.test

 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

 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@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

-# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-#PKGNAME#: script-with-language-extension usr/bin/*.*

debian/patches/fix_bashism.patch

+Author: Andreas Tille <tille@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

+fix_bashism.patch

debian/tests/run-unit-test

 #!/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

+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

+debian/README.test

debian/upstream/metadata

 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