[med-svn] [Git][med-team/busco][master] 3 commits: Updated Autopkgtest for auto data download

Israel Komolehin (@Komolehin) gitlab at salsa.debian.org
Tue Dec 19 12:24:47 GMT 2023 


Israel Komolehin pushed to branch master at Debian Med / busco


Commits:
9e542a57 by Komolehin Israel Timilehin at 2023-12-19T12:20:21+00:00
Updated Autopkgtest for auto data download

- - - - -
0848eb14 by Komolehin Israel Timilehin at 2023-12-19T12:23:43+00:00
Updated debian/copyright

- - - - -
b4fa1aa0 by Komolehin Israel Timilehin at 2023-12-19T12:24:06+00:00
Updated debian/changelog

- - - - -


5 changed files:

- debian/changelog
- debian/copyright
- − debian/tests/data/README.md
- − debian/tests/data/bacteria_odb10.2020-03-06.tar.gz
- debian/tests/run-unit-test-2


Changes:

=====================================
debian/changelog
=====================================
@@ -2,8 +2,7 @@ busco (5.5.0-2) UNRELEASED; urgency=medium
 
   
   * Added autopkgtest to check hmmer and prodigal integration (Closes: #1010653)
-  * Updated copyright
-
+  
  -- Komolehin Israel Timilehin <komolehinisrael at gmail.com>  Fri, 15 Dec 2023 17:09:43 +0000
 
 busco (5.5.0-1) unstable; urgency=medium


=====================================
debian/copyright
=====================================
@@ -10,11 +10,6 @@ Files: debian/*
 Copyright: 2020 Andreas Tille <tille at debian.org>
 License: MIT
 
-Files: debian/tests/data/*
-Copyright: Busco
-Source: wget https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz
-Licence: CC-BY-ND-4.0
-
 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
@@ -32,74 +27,4 @@ License: MIT
  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.
-
-Licence: CC-BY-ND-4.0
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\ No newline at end of file
+ SOFTWARE.
\ No newline at end of file


=====================================
debian/tests/data/README.md deleted
=====================================
@@ -1,4 +0,0 @@
-Test for busco
-
-The data for the test can be referenced from:
-        https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz
\ No newline at end of file


=====================================
debian/tests/data/bacteria_odb10.2020-03-06.tar.gz deleted
=====================================
Binary files a/debian/tests/data/bacteria_odb10.2020-03-06.tar.gz and /dev/null differ


=====================================
debian/tests/run-unit-test-2
=====================================
@@ -20,10 +20,14 @@ cp -a /usr/share/doc/${pkg}/examples/genome.fna .
 
 
 # Extract lineage
-tar -xzf bacteria_odb10.2020-03-06.tar.gz
+
 
 # This test requires Prodigal and HMMER
-$pkg -m genome -i genome.fna -o test_bacteria -l ./bacteria_odb10
+# Busco will automatically download and version the dataset for the specified lineage
+$pkg -m genome -i genome.fna -o test_bacteria -l bacteria_odb10
+
+
+ls
 
 # Check output directory
 if [ -d "./test_bacteria" ]; then



View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/2119ef11403ac4bab6d784b2ad9b43494021e0d0...b4fa1aa05aa036d2ce9df50f2f31c52e2a2ba6ee

-- 
View it on GitLab: https://salsa.debian.org/med-team/busco/-/compare/2119ef11403ac4bab6d784b2ad9b43494021e0d0...b4fa1aa05aa036d2ce9df50f2f31c52e2a2ba6ee
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