[med-svn] [kraken] 04/06: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository kraken.

commit 65a107d2040e57fb900ce0531049b39fb16ef129
Author: Andreas Tille <tille at debian.org>
Date:   Mon Nov 13 16:35:36 2017 +0100

    Adapt patches
---
 debian/patches/kraken_tmp_dir.patch |  2 +-
 debian/patches/use_jellyfish1.patch | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/debian/patches/kraken_tmp_dir.patch b/debian/patches/kraken_tmp_dir.patch
index a69c1e7..455503a 100644
--- a/debian/patches/kraken_tmp_dir.patch
+++ b/debian/patches/kraken_tmp_dir.patch
@@ -7,7 +7,7 @@ Description: Some changes needed to differentiate packaging target dir and
 +++ b/install_kraken.sh
 @@ -21,7 +21,7 @@ set -e
  
- VERSION="0.10.5-beta"
+ VERSION="1.0"
  
 -if [ -z "$1" ] || [ -n "$2" ]
 +if [ -z "$1" ] # || [ -n "$2" ]
diff --git a/debian/patches/use_jellyfish1.patch b/debian/patches/use_jellyfish1.patch
index 87f612b..2a20689 100644
--- a/debian/patches/use_jellyfish1.patch
+++ b/debian/patches/use_jellyfish1.patch
@@ -3,11 +3,11 @@ 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 @@
+--- a/scripts/build_kraken_db.sh
++++ b/scripts/build_kraken_db.sh
+@@ -78,13 +78,13 @@ else
  
-   find library/ '(' -name '*.fna' -o -name '*.fa' -o -name '*.ffn' ')' -print0 | \
+   find library/ -name '*.fna' -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 \
@@ -21,9 +21,9 @@ Last-Update: 2017-08-10
    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 @@
+--- a/scripts/check_for_jellyfish.sh
++++ b/scripts/check_for_jellyfish.sh
+@@ -24,7 +24,7 @@ set -u  # Protect against uninitialized
  set -e  # Stop on error
  set -o pipefail  # Stop on failures in non-final pipeline commands
  

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