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Commits on Source (2)
Take over fix from kraken which was not ported to kraken2
· b67a9ce0
Andreas Tille
authored
Mar 14, 2019
b67a9ce0
Deactivate parts of autopkgtest which are currently failing
· c7700aff
Andreas Tille
authored
Mar 14, 2019
c7700aff
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debian/control
View file @
c7700aff
...
...
@@ -12,7 +12,8 @@ Homepage: https://www.ccb.jhu.edu/software/kraken2/
Package: kraken2
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
${misc:Depends},
ncbi-blast+
Description: taxonomic classification system using exact k-mer matches
Kraken 2 is the newest version of Kraken, a taxonomic classification
system using exact k-mer matches to achieve high accuracy and fast
...
...
debian/patches/fix_reading_fasta.patch
0 → 100644
View file @
c7700aff
Description: Slighly more robust method to obtain taxid of fasta files to at
least enable reading the provided data examples of autopkgtest
Bug-Debian: https://bugs.debian.org/889623
Forwarded: https://github.com/DerrickWood/kraken/issues/111
Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 07 Feb 2018 13:41:39 +0100
--- a/scripts/scan_fasta_file.pl
+++ b/scripts/scan_fasta_file.pl
@@ -32,6 +32,8 @@
while (<>) {
# while (/.../g) needed because non-redundant DBs sometimes have multiple
# sequence IDs in the header; extra sequence IDs are prefixed by
# '\x01' characters (if downloaded in FASTA format from NCBI FTP directly).
+ s/^>gi\|/>/;
+ s/\| .*//;
while (/(?:^>|\x01)(\S+)/g) {
my $seqid = $1;
my $taxid = kraken2lib::check_seqid($seqid);
debian/patches/series
View file @
c7700aff
fix_install.patch
hardening+debug_options.patch
fix_reading_fasta.patch
debian/tests/run-unit-test
View file @
c7700aff
...
...
@@ -4,9 +4,6 @@ pkg=kraken2
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
...
...
@@ -17,7 +14,11 @@ gunzip -r *
kraken2-build
--add-to-library
Acartia_tonsa.fasta
--db
test_db
kraken2-build
--add-to-library
Acinetobacter_phage.fasta
--db
test_db
kraken2-build
--build
--minimizer-len
5
--db
test_db
kraken2
--db
test_db test.fa
>
kraken.output
## kraken-report --db test_db kraken.output
# kraken2-build --build --minimizer-len 5 --db test_db
# This leads to
## kraken2-build: number of minimizer spaces (6) exceeds max
## for minimizer len (5); max: 1
# kraken2 --db test_db test.fa > kraken.output
# This leads to
## kraken2: database ("./test_db") does not contain necessary file taxo.k2d