[med-svn] r22489 - trunk/packages/phylophlan/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2016-07-11 19:31:03 +0000 (Mon, 11 Jul 2016)
New Revision: 22489

Added:
   trunk/packages/phylophlan/trunk/debian/patches/absolute_path_taxcuration.patch
   trunk/packages/phylophlan/trunk/debian/patches/create_dir.patch
Modified:
   trunk/packages/phylophlan/trunk/debian/patches/series
Log:
Deal with some install issues and pathes


Added: trunk/packages/phylophlan/trunk/debian/patches/absolute_path_taxcuration.patch
===================================================================
--- trunk/packages/phylophlan/trunk/debian/patches/absolute_path_taxcuration.patch	                        (rev 0)
+++ trunk/packages/phylophlan/trunk/debian/patches/absolute_path_taxcuration.patch	2016-07-11 19:31:03 UTC (rev 22489)
@@ -0,0 +1,15 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Use absolute path to taxcuration dir
+
+--- a/phylophlan.py
++++ b/phylophlan.py
+@@ -719,7 +719,7 @@ def circlader( proj, integrate, tax = No
+     #info("Generating tree output images ...")
+     c_circ = "circlader/circlader.py"
+     c_circ_an = "circlader/circlader_annotate.py"
+-    c_reroot = "./taxcuration/tree_reroot.py"
++    c_reroot = os.path.join(os.path.dirname(os.path.realpath(__file__)), "taxcuration/tree_reroot.py")
+ 
+     names = [l.strip().split('\t')[0] for l in open(dat_fol+ors2prots)]
+ 

Added: trunk/packages/phylophlan/trunk/debian/patches/create_dir.patch
===================================================================
--- trunk/packages/phylophlan/trunk/debian/patches/create_dir.patch	                        (rev 0)
+++ trunk/packages/phylophlan/trunk/debian/patches/create_dir.patch	2016-07-11 19:31:03 UTC (rev 22489)
@@ -0,0 +1,51 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 23 May 2016 16:09:13 +0200
+Description: Do not require user to create output dir hierarchy in advance
+
+--- a/phylophlan.py
++++ b/phylophlan.py
+@@ -209,7 +209,7 @@ def get_inputs(proj):
+               "[No more than one txt file (the taxonomy for taxonomic analysis) allowed" )
+ 
+     if not os.path.isdir(dat_fol):
+-        os.mkdir( dat_fol )
++        os.makedirs( dat_fol )
+ 
+     if not os.path.exists(dat_fol + ors2prots):
+         with open(dat_fol + ors2prots, 'w') as outf:
+@@ -282,7 +282,7 @@ def faa2ppafaa( inps, nproc, proj ):
+     pool = mp.Pool( nproc )
+     mmap = [(inp_fol+i+'.faa', dat_fol+i+'.b6o') for i in inps if not os.path.exists(dat_fol+i+'.b6o')]
+ 
+-    if not os.path.isdir(dat_fol): os.mkdir(dat_fol) # create the tmp directory if does not exists
++    if not os.path.isdir(dat_fol): os.makedirs(dat_fol) # create the tmp directory if does not exists
+ 
+     if not mmap:
+         info("All usearch runs already performed!\n")
+@@ -333,7 +333,7 @@ def blast(inps, nproc, proj, blast_full=
+     pool = mp.Pool(nproc)
+     mmap = [(inp_fol+i+'.fna', dat_fol+i+'.b6o') for i in inps if not os.path.exists(dat_fol+i+'.b6o')]
+ 
+-    if not os.path.isdir(dat_fol): os.mkdir(dat_fol) # create the tmp directory if does not exists
++    if not os.path.isdir(dat_fol): os.makedirs(dat_fol) # create the tmp directory if does not exists
+ 
+     if not mmap:
+         info('All tblastn runs already performed!\n')
+@@ -421,7 +421,7 @@ def gens2prots(inps, proj ):
+     inp_fol = "input/"+proj+"/"
+     dat_fol = "data/"+proj+"/usearch/"
+ 
+-    if not os.path.isdir(dat_fol): os.mkdir(dat_fol) # create the tmp directory if does not exists
++    if not os.path.isdir(dat_fol): os.makedirs(dat_fol) # create the tmp directory if does not exists
+ 
+     if os.path.exists( dat_fol+ups2faa_pkl ):
+         return
+@@ -666,7 +666,7 @@ def fasttree( proj, integrate ):
+     dat_fol = "data/"+proj+"/"
+     outt = out_fol+proj+"."+ ( o_inttree if integrate else o_tree)
+     if not os.path.isdir(out_fol):
+-        os.mkdir( out_fol )
++        os.makedirs( out_fol )
+     aln_in = dat_fol+aln_int_tot if integrate else dat_fol+aln_tot
+     if os.path.exists( outt ):
+         info("Final tree already built ("+outt+")!\n")

Modified: trunk/packages/phylophlan/trunk/debian/patches/series
===================================================================
--- trunk/packages/phylophlan/trunk/debian/patches/series	2016-07-11 16:07:37 UTC (rev 22488)
+++ trunk/packages/phylophlan/trunk/debian/patches/series	2016-07-11 19:31:03 UTC (rev 22489)
@@ -2,3 +2,5 @@
 datadir.patch
 use_vsearch.patch
 fasttree_name.patch
+create_dir.patch
+absolute_path_taxcuration.patch