[med-svn] [dnaclust] 01/02: Fix name space conflict with mira-assembler

[Andreas Tille]

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tille pushed a commit to branch master
in repository dnaclust.

commit abb9aae1ed2771cd36361dd5a8d1028021822707
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 11 10:24:24 2014 +0100

    Fix name space conflict with mira-assembler
---
 debian/install                                     |  2 +-
 .../resolve_name_space_conflict_fastasort.patch    | 36 ++++++++++++++++++++++
 2 files changed, 37 insertions(+), 1 deletion(-)

diff --git a/debian/install b/debian/install
index a19dbb0..e61545a 100644
--- a/debian/install
+++ b/debian/install
@@ -1,7 +1,7 @@
 dnaclust			usr/bin
 dnaclust-abun.sh		usr/bin
 dnaclust-ref			usr/bin
-fastaselect			usr/bin
+fastaselect			usr/lib/dnaclust
 fastasort			usr/lib/dnaclust
 find-large-clusters		usr/bin
 generate_test_clusters.sh	usr/bin
diff --git a/debian/patches/resolve_name_space_conflict_fastasort.patch b/debian/patches/resolve_name_space_conflict_fastasort.patch
index 53af771..fc15b4c 100644
--- a/debian/patches/resolve_name_space_conflict_fastasort.patch
+++ b/debian/patches/resolve_name_space_conflict_fastasort.patch
@@ -32,6 +32,15 @@ Description: Set explicit PATH for fastasor to /usr/lib/dnaclust to avoid
  
  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
+@@ -87,7 +87,7 @@ then
+   unclustered_seq=`basename $input .fasta`.unclustered.fasta
+   awk '{ for (i = 1; i <= NF; i++) print $i}' $input.db.clusters > $tempdir/clustered_seqs
+ 
+-  "$dnaclust_path/fastaselect" --everything-except -f ${input} < $tempdir/clustered_seqs > $tempdir/${unclustered_seq}
++  "/usr/lib/dnaclust/fastaselect" --everything-except -f ${input} < $tempdir/clustered_seqs > $tempdir/${unclustered_seq}
+   if [[ -s $tempdir/${unclustered_seq} ]] ; then
+     "$dnaclust_path/dnaclust" $parameters -s $similarity -t $threads --no-k-mer-filter -i $tempdir/${unclustered_seq} > $input.denovo.clusters  
+     print_message "Writing de novo clusters to: $input.denovo.clusters"
 --- a/find-large-clusters
 +++ b/find-large-clusters
 @@ -54,7 +54,7 @@ tempdir=`mktemp -d -p .`
@@ -43,3 +52,30 @@ Description: Set explicit PATH for fastasor to /usr/lib/dnaclust to avoid
  
  input_count=`grep -c '^>' $sequences_sorted`
  if [ $input_count -le 1 ]
+@@ -82,10 +82,10 @@ print_message "Clustering the set of sam
+     | awk --assign=minimum=$minimum_cluster_size '{if (NF >= minimum) print $0}' > $large_clusters
+ 
+ sequences_sorted_head_large_centers=`mktemp -p $tempdir`
+-"$dnaclust_path/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
++"/usr/lib/dnaclust/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
+ 
+ sequences_minus_centers=`mktemp -p $tempdir`
+-"$dnaclust_path/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
++"/usr/lib/dnaclust/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
+ 
+ centers_count=`grep -c '^>' $sequences_sorted_head_large_centers`
+ print_message "Recruiting from the rest of the sequences, using $centers_count centers."
+--- a/star-align
++++ b/star-align
+@@ -38,7 +38,7 @@ sequences_fasta=`mktemp -p $tempdir`
+ 
+ while read line
+ do
+-    echo $line | "$dnaclust_path/fastaselect" -f $input_fasta --cluster-centers > $center_fasta
+-    echo $line | "$dnaclust_path/fastaselect" -f $input_fasta --cluster-sequences > $sequences_fasta
++    echo $line | "/usr/lib/dnaclust/fastaselect" -f $input_fasta --cluster-centers > $center_fasta
++    echo $line | "/usr/lib/dnaclust/fastaselect" -f $input_fasta --cluster-sequences > $sequences_fasta
+     "$dnaclust_path/dnaclust" -s $similarity --multiple-alignment --no-k-mer-filter -i $sequences_fasta -p $center_fasta -r
+-done
+\ No newline at end of file
++done

-- 
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