[med-svn] [kraken] 01/01: use jellyfish1

[Nadiya Sitdykova]

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rovenskasa-guest pushed a commit to branch master
in repository kraken.

commit 5af662a3fdbf50ac3a59338bc37263fd3499545e
Author: Nadiya Sitdykova <rovenskasa at gmail.com>
Date:   Thu Aug 10 15:54:21 2017 -0400

    use jellyfish1
---
 debian/changelog                    |  1 +
 debian/control                      |  2 +-
 debian/patches/series               |  1 +
 debian/patches/use_jellyfish1.patch | 34 ++++++++++++++++++++++++++++++++++
 4 files changed, 37 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 20c528f..e14c0e1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -5,6 +5,7 @@ kraken (0.10.5~beta-4) UNRELEASED; urgency=medium
 
   * Add autopkgtest test-suite
   * Fix version of dependency: jellyfish (= 1.1.5-1)
+  * Fix dependency from jellyfish to jellyfish1
 
   * debian/upstream/metadata: Added ref to bio.tools (Steffen Moeller)
   * debian/control: Policy bump to 4.0.1 (Steffen Moeller)
diff --git a/debian/control b/debian/control
index 8061fa8..6dd37bd 100644
--- a/debian/control
+++ b/debian/control
@@ -13,7 +13,7 @@ Package: kraken
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         jellyfish (= 1.1.5-1)
+         jellyfish1
 Description: assigning taxonomic labels to short DNA sequences
  Kraken is a system for assigning taxonomic labels to short DNA
  sequences, usually obtained through metagenomic studies. Previous
diff --git a/debian/patches/series b/debian/patches/series
index 1cb33b0..e264766 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+use_jellyfish1.patch
 kraken_tmp_dir.patch
diff --git a/debian/patches/use_jellyfish1.patch b/debian/patches/use_jellyfish1.patch
new file mode 100644
index 0000000..87f612b
--- /dev/null
+++ b/debian/patches/use_jellyfish1.patch
@@ -0,0 +1,34 @@
+Author: Nadiya Sitdykova
+Description: change call of jellyfish to call of jellyfish1
+Last-Update: 2017-08-10
+
+===========================================================
+--- kraken.orig/scripts/build_kraken_db.sh
++++ kraken/scripts/build_kraken_db.sh
+@@ -78,13 +78,13 @@
+ 
+   find library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -print0 | \
+     xargs -0 cat | \
+-    jellyfish count -m $KRAKEN_KMER_LEN -s $KRAKEN_HASH_SIZE -C -t $KRAKEN_THREAD_CT \
++    jellyfish1 count -m $KRAKEN_KMER_LEN -s $KRAKEN_HASH_SIZE -C -t $KRAKEN_THREAD_CT \
+       -o database /dev/fd/0
+ 
+   # Merge only if necessary
+   if [ -e "database_1" ]
+   then
+-    jellyfish merge -o database.jdb.tmp database_*
++    jellyfish1 merge -o database.jdb.tmp database_*
+   else
+     mv database_0 database.jdb.tmp
+   fi
+--- kraken.orig/scripts/check_for_jellyfish.sh
++++ kraken/scripts/check_for_jellyfish.sh
+@@ -24,7 +24,7 @@
+ set -e  # Stop on error
+ set -o pipefail  # Stop on failures in non-final pipeline commands
+ 
+-JELLYFISH_VERSION=$(jellyfish --version | awk '{print $2}')
++JELLYFISH_VERSION=$(jellyfish1 --version | awk '{print $2}')
+ if [[ $JELLYFISH_VERSION =~ ^1\. ]]
+ then
+   echo "Found jellyfish v$JELLYFISH_VERSION"

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