[med-svn] [Git][med-team/flye][master] 2 commits: Create some hopefully sensible test once flye is supposed to work

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / flye


Commits:
f7951c65 by Andreas Tille at 2020-06-28T08:30:02+02:00
Create some hopefully sensible test once flye is supposed to work

- - - - -
deb022a0 by Andreas Tille at 2020-06-28T08:30:52+02:00
Add todo

- - - - -


3 changed files:

- debian/changelog
- + debian/tests/data/get
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,7 +1,7 @@
 flye (2.7.1+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #962292)
-  
-  Wait for https://github.com/fenderglass/Flye/issues/275 to be resolved.
+  TODO: See https://github.com/fenderglass/Flye/issues/275
+        Wait until minimap2 patch is applied
 
  -- Andreas Tille <tille at debian.org>  Fri, 05 Jun 2020 15:05:08 +0200


=====================================
debian/tests/data/get
=====================================
@@ -0,0 +1,5 @@
+#!/bin/sh
+# see docs/USAGE.md
+wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta
+
+# FIXME: I'm hesitating to include such a big dataset here


=====================================
debian/tests/run-unit-test
=====================================
@@ -6,14 +6,21 @@ pkg=#PACKAGENAME#
 export LC_ALL=C.UTF-8
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  # Double quote below to expand the temporary directory variable now versus
-  # later is on purpose.
-  # shellcheck disable=SC2064
   trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
 cd "${AUTOPKGTEST_TMP}"
 
-#do_stuff_to_test_package#
+if [ "${REALLYRUNTEST}" = "yes" ] ; then
+# From docs/USAGE.md:
+
+wget https://zenodo.org/record/1172816/files/E.coli_PacBio_40x.fasta
+flye --pacbio-raw E.coli_PacBio_40x.fasta --out-dir out_pacbio --genome-size 5m --threads 4
+
+wget https://zenodo.org/record/1172816/files/Loman_E.coli_MAP006-1_2D_50x.fasta
+flye --nano-raw Loman_E.coli_MAP006-1_2D_50x.fasta --out-dir out_nano --genome-size 5m --threads 4
+
+else
+  flye --help
+  echo 'Test is downloading large databases.  Set "REALLYRUNTEST=yes" to run this test'
+fi



View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77

-- 
View it on GitLab: https://salsa.debian.org/med-team/flye/-/compare/d6c7122a1772197bbf454abf0efb4efff35c6687...deb022a09f4f81555cd814e80fb1d573600d7e77
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