[med-svn] r22635 - in trunk/packages/metaphlan2/trunk/debian: . bin patches

[Andreas Tille]

Author: tille
Date: 2016-07-26 08:23:16 +0000 (Tue, 26 Jul 2016)
New Revision: 22635

Added:
   trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2
Removed:
   trunk/packages/metaphlan2/trunk/debian/links
Modified:
   trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch
Log:
Fix typos and use wrapper instead of link since script location is used in code


Added: trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2	                        (rev 0)
+++ trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2	2016-07-26 08:23:16 UTC (rev 22635)
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+cmd=`basename "$0" .py`.py
+
+exec "/usr/share/metaphlan2/$cmd" "$@"


Property changes on: trunk/packages/metaphlan2/trunk/debian/bin/metaphlan2
___________________________________________________________________
Added: svn:executable
   + *

Deleted: trunk/packages/metaphlan2/trunk/debian/links
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/links	2016-07-26 07:24:31 UTC (rev 22634)
+++ trunk/packages/metaphlan2/trunk/debian/links	2016-07-26 08:23:16 UTC (rev 22635)
@@ -1,2 +0,0 @@
-usr/share/metaphlan2/metaphlan2.py		usr/bin/metaphlan2
-

Modified: trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch
===================================================================
--- trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch	2016-07-26 07:24:31 UTC (rev 22634)
+++ trunk/packages/metaphlan2/trunk/debian/patches/mpa_dir-is-usr_share_metaphlan2.patch	2016-07-26 08:23:16 UTC (rev 22635)
@@ -1,7 +1,7 @@
 Author: Andreas Tille <tille at debian.org>
 Last-Update: Mon, 23 May 2016 16:09:13 +0200
 Description: Instead of setting mpa_dir bash variable the path to the
- database files in /usr/share/metahplan2 is set explicitly.
+ database files in /usr/share/metaphlan2 is set explicitly.
  .
  The doc is also adapted to this change.
 
@@ -12,7 +12,7 @@
              "*  You can also provide an externally BowTie2-mapped SAM if you specify this format with \n"
              "   --input_type. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the obtained sam:\n"
 -            "$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/db_v20/mpa_v20_m200 -U metagenome.fastq\n"
-+            "$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metahplan2/db_v20/mpa_v20_m200 -U metagenome.fastq\n"
++            "$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metaphlan2/db_v20/mpa_v20_m200 -U metagenome.fastq\n"
              "$ metaphlan2.py metagenome.sam --input_type sam > profiled_metagenome.txt\n\n"
              
              "*  Multiple alternative ways to pass the input are also available:\n"
@@ -21,7 +21,7 @@
      if not os.path.isfile(pars['mpa_pkl']):
          sys.stderr.write("Error: Unable to find the mpa_pkl file at: " + pars['mpa_pkl'] +
 -                         "\nExpecting location ${mpa_dir}/db_v20/map_v20_m200.pkl "
-+                         "\nExpecting location /usr/share/metahplan2/db_v20/map_v20_m200.pkl "
++                         "\nExpecting location /usr/share/metaphlan2/db_v20/mpa_v20_m200.pkl "
                           "\nSelect the file location with the option --mpa_pkl.\n"
                           "Exiting...\n\n")
          sys.exit(1)           
@@ -30,7 +30,7 @@
                                "[--bowtie2db option]! "
                                "(or wrong path provided)."
 -                              "\nExpecting location ${mpa_dir}/db_v20/map_v20_m200 "
-+                              "\nExpecting location /usr/share/metahplan2/db_v20/map_v20_m200 "
++                              "\nExpecting location /usr/share/metaphlan2/db_v20/mpa_v20_m200 "
                                "\nExiting... " )
              sys.exit(1)
  
@@ -78,7 +78,7 @@
  #!cmd
 -$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/db_v20/mpa_v20_m200 -U metagenome.fastq
 -$ metaphlan2.py metagenome.sam --input_type sam > profiled_metagenome.txt
-+$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metahplan2/db_v20/mpa_v20_m200 -U metagenome.fastq
++$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metaphlan2/db_v20/mpa_v20_m200 -U metagenome.fastq
 +$ metaphlan2 metagenome.sam --input_type sam > profiled_metagenome.txt
  ```
  
@@ -93,7 +93,7 @@
  ```
  #!cmd
 -$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2.py --input_type fastq --bowtie2db ${mpa_dir}/db_v20/mpa_v20_m200 > profiled_metagenome.txt
-+$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2 --input_type fastq --bowtie2db /usr/share/metahplan2/db_v20/mpa_v20_m200 > profiled_metagenome.txt
++$ tar xjf metagenome.tar.bz2 --to-stdout | metaphlan2 --input_type fastq --bowtie2db /usr/share/metaphlan2/db_v20/mpa_v20_m200 > profiled_metagenome.txt
  ```
  
  ```
@@ -163,7 +163,7 @@
     --input_type. Two steps: first apply BowTie2 and then feed MetaPhlAn2 with the obtained sam:
 -$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/db_v20/mpa_v20_m200 -U metagenome.fastq
 -$ metaphlan2.py metagenome.sam --input_type sam > profiled_metagenome.txt
-+$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metahplan2/db_v20/mpa_v20_m200 -U metagenome.fastq
++$ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x /usr/share/metaphlan2/db_v20/mpa_v20_m200 -U metagenome.fastq
 +$ metaphlan2 metagenome.sam --input_type sam > profiled_metagenome.txt
  
  *  Multiple alternative ways to pass the input are also available:
@@ -227,7 +227,7 @@
      echo "Running metaphlan2 on ${f}"
      bn=$(basename ${f} | cut -d . -f 1)
 -    tar xjfO ${f} | ../metaphlan2.py --bowtie2db ../db_v20/mpa_v20_m200 --mpa_pkl ../db_v20/mpa_v20_m200.pkl --input_type multifastq --nproc 10 -s sams/${bn}.sam.bz2 --bowtie2out sams/${bn}.bowtie2_out.bz2 -o sams/${bn}.profile
-+    tar xjfO ${f} | metaphlan2 --bowtie2db /usr/share/metahplan2/db_v20/mpa_v20_m200 --mpa_pkl /usr/share/metahplan2/db_v20/mpa_v20_m200.pkl --input_type multifastq --nproc 10 -s sams/${bn}.sam.bz2 --bowtie2out sams/${bn}.bowtie2_out.bz2 -o sams/${bn}.profile
++    tar xjfO ${f} | metaphlan2 --bowtie2db /usr/share/metaphlan2/db_v20/mpa_v20_m200 --mpa_pkl /usr/share/metaphlan2/db_v20/mpa_v20_m200.pkl --input_type multifastq --nproc 10 -s sams/${bn}.sam.bz2 --bowtie2out sams/${bn}.bowtie2_out.bz2 -o sams/${bn}.profile
  done
  ```