[med-svn] [Git][med-team/kallisto][master] Add test

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / kallisto


Commits:
ef79f00f by Andreas Tille at 2019-03-23T06:30:09Z
Add test

- - - - -


7 changed files:

- debian/README.test
- debian/control
- + debian/kallisto-examples.docs
- + debian/kallisto-examples.install
- + debian/kallisto.docs
- + debian/kallisto.install
- debian/tests/run-unit-test


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 installing the package kallisto-examples
+and running the provided test:
 
     sh run-unit-test
 


=====================================
debian/control
=====================================
@@ -17,8 +17,8 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: near-optimal RNA-Seq quantification
- Kallisto is a program for quantifying abundances of transcripts from RNA-
- Seq data, or more generally of target sequences using high-throughput
+ Kallisto is a program for quantifying abundances of transcripts from
+ RNA-Seq data, or more generally of target sequences using high-throughput
  sequencing reads. It is based on the novel idea of pseudoalignment for
  rapidly determining the compatibility of reads with targets, without the
  need for alignment. On benchmarks with standard RNA-Seq data, kallisto
@@ -30,3 +30,25 @@ Description: near-optimal RNA-Seq quantification
  quantification tools. In fact, because the pseudoalignment procedure is
  robust to errors in the reads, in many benchmarks kallisto significantly
  outperforms existing tools.
+
+Package: kallisto-examples
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: kallisto
+Suggests: snakemake
+Description: near-optimal RNA-Seq quantification (example data)
+ Kallisto is a program for quantifying abundances of transcripts from
+ RNA-Seq data, or more generally of target sequences using high-throughput
+ sequencing reads. It is based on the novel idea of pseudoalignment for
+ rapidly determining the compatibility of reads with targets, without the
+ need for alignment. On benchmarks with standard RNA-Seq data, kallisto
+ can quantify 30 million human reads in less than 3 minutes on a Mac
+ desktop computer using only the read sequences and a transcriptome index
+ that itself takes less than 10 minutes to build. Pseudoalignment of
+ reads preserves the key information needed for quantification, and
+ kallisto is therefore not only fast, but also as accurate than existing
+ quantification tools. In fact, because the pseudoalignment procedure is
+ robust to errors in the reads, in many benchmarks kallisto significantly
+ outperforms existing tools.
+ .
+ This package contains usage examples which are used in autopkgtest.


=====================================
debian/kallisto-examples.docs
=====================================
@@ -0,0 +1 @@
+debian/tests/run-unit-test


=====================================
debian/kallisto-examples.install
=====================================
@@ -0,0 +1 @@
+test	usr/share/doc/kallisto


=====================================
debian/kallisto.docs
=====================================
@@ -0,0 +1 @@
+debian/README.test


=====================================
debian/kallisto.install
=====================================
@@ -0,0 +1 @@
+usr


=====================================
debian/tests/run-unit-test
=====================================
@@ -1,7 +1,7 @@
 #!/bin/bash
 set -e
 
-pkg=#PACKAGENAME#
+pkg=kallisto
 
 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
   AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
@@ -11,8 +11,27 @@ if [ "${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 "${AUTOPKGTEST_TMP}"
+cd "${AUTOPKGTEST_TMP}"/test
 
-#do_stuff_to_test_package#
+# OK
+kallisto index -i transcripts.kidx transcripts.fasta.gz
+kallisto quant -i transcripts.kidx -b 30 -o kallisto_out --genomebam --gtf transcripts.gtf.gz --chromosomes chrom.txt reads_1.fastq.gz reads_2.fastq.gz
+
+exit 0
+
+# The following command line is wrong but it should not throw Segmentation fault!
+
+ $ LC_ALL=C kallisto quant -i transcripts.kidx -b 30 -o kallisto_out --genomebam --gtf transcripts.gtf.gz transcripts.fasta.gz --chromosomes reads_1.fastq.gz reads_2.fastq.gz
+
+[quant] fragment length distribution will be estimated from the data
+[index] k-mer length: 31
+[index] number of targets: 14
+[index] number of k-mers: 22,118
+[index] number of equivalence classes: 20
+Warning: could not find chromosomes for 117 transcripts
+[quant] running in paired-end mode
+[quant] will process pair 1: transcripts.fasta.gz
+                             reads_2.fastq.gz
+[quant] finding pseudoalignments for the reads ...Segmentation fault



View it on GitLab: https://salsa.debian.org/med-team/kallisto/commit/ef79f00fdc760bf4e6e0d0195acce17f44b633f8

-- 
View it on GitLab: https://salsa.debian.org/med-team/kallisto/commit/ef79f00fdc760bf4e6e0d0195acce17f44b633f8
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