[med-svn] [dnaclust] 03/03: Resolve name space conflict with fastasort which is also in exonerate. TODO: fastaselect is also in mira-assembler -> will choose the same approach

[Andreas Tille]

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tille pushed a commit to branch master
in repository dnaclust.

commit 3cc9289993fbcfcd641126932a382fbd6f6c1b19
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 11 10:16:14 2014 +0100

    Resolve name space conflict with fastasort which is also in exonerate.  TODO: fastaselect is also in mira-assembler -> will choose the same approach
---
 debian/changelog                                   |  8 ++++
 debian/install                                     |  2 +-
 .../resolve_name_space_conflict_fastasort.patch    | 45 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 4 files changed, 55 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 1edf711..3f1cf55 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+dnaclust (3-2) UNRELEASED; urgency=medium
+
+  * Move /usr/bin/fastasor to /usr/lib/dnaclust/fastasor to avoid
+    name space conflict with exonerate.
+    Closes: #737913
+
+ -- Andreas Tille <tille at debian.org>  Tue, 11 Feb 2014 10:02:25 +0100
+
 dnaclust (3-1) unstable; urgency=low
 
   * Initial release (Closes: #737327)
diff --git a/debian/install b/debian/install
index b4ce480..a19dbb0 100644
--- a/debian/install
+++ b/debian/install
@@ -2,7 +2,7 @@ dnaclust			usr/bin
 dnaclust-abun.sh		usr/bin
 dnaclust-ref			usr/bin
 fastaselect			usr/bin
-fastasort			usr/bin
+fastasort			usr/lib/dnaclust
 find-large-clusters		usr/bin
 generate_test_clusters.sh	usr/bin
 star-align			usr/bin
diff --git a/debian/patches/resolve_name_space_conflict_fastasort.patch b/debian/patches/resolve_name_space_conflict_fastasort.patch
new file mode 100644
index 0000000..53af771
--- /dev/null
+++ b/debian/patches/resolve_name_space_conflict_fastasort.patch
@@ -0,0 +1,45 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 11 Feb 2014 10:02:25 +0100
+Bug-Debian: http://bugs.debian.org/737913
+Description: Set explicit PATH for fastasor to /usr/lib/dnaclust to avoid
+  name space conflict with exonerate.
+
+--- a/dnaclust-abun.sh
++++ b/dnaclust-abun.sh
+@@ -67,8 +67,8 @@ trap "rm -fr $tempdir" EXIT
+ db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
+ # Reads the sequences from STDIN.
+ print_message "Reading and sorting the database sequences: $tempdir/${db_sorted}" 
+-#"$dnaclust_path/fastasort" --random-shuffle > $sequences_sorted 
+-cat $cluster_centers | "$dnaclust_path/fastasort" > $tempdir/${db_sorted}
++#"/usr/lib/dnaclust/fastasort" --random-shuffle > $sequences_sorted 
++cat $cluster_centers | "/usr/lib/dnaclust/fastasort" > $tempdir/${db_sorted}
+ 
+ print_message "Recruiting from the sequences, using database."
+-"$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $input -p $tempdir/${db_sorted} -r | awk '{if (NF > 1) print $0}' > $input.db.clusters
+\ No newline at end of file
++"$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $input -p $tempdir/${db_sorted} -r | awk '{if (NF > 1) print $0}' > $input.db.clusters
+--- a/dnaclust-ref
++++ b/dnaclust-ref
+@@ -74,8 +74,8 @@ trap "rm -fr $tempdir" EXIT
+ db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
+ # Reads the sequences from STDIN.
+ print_message "Reading and sorting the database sequences: $tempdir/${db_sorted}" 
+-#"$dnaclust_path/fastasort" --random-shuffle > $sequences_sorted 
+-cat $cluster_centers | "$dnaclust_path/fastasort" > $tempdir/${db_sorted}
++#"/usr/lib/dnaclust/fastasort" --random-shuffle > $sequences_sorted 
++cat $cluster_centers | "/usr/lib/dnaclust/fastasort" > $tempdir/${db_sorted}
+ 
+ print_message "Recruiting from the sequences, using database."
+ "$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $input -p $tempdir/${db_sorted} -r | awk '{if (NF > 1) print $0}' > $input.db.clusters
+--- a/find-large-clusters
++++ b/find-large-clusters
+@@ -54,7 +54,7 @@ tempdir=`mktemp -d -p .`
+ sequences_sorted=`mktemp -p $tempdir`
+ # Reads the sequences from STDIN.
+ print_message "Reading and sorting the input sequences."
+-"$dnaclust_path/fastasort" --random-shuffle > $sequences_sorted 
++"/usr/lib/dnaclust/fastasort" --random-shuffle > $sequences_sorted 
+ 
+ input_count=`grep -c '^>' $sequences_sorted`
+ if [ $input_count -le 1 ]
diff --git a/debian/patches/series b/debian/patches/series
index c0510e7..febaaec 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 fix_shel_path.patch
 do_not_staically_linking.patch
+resolve_name_space_conflict_fastasort.patch

-- 
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