[med-svn] [Git][med-team/graphbin][master] Patch to change python files that graphbin invokes to the ones under /usr/share/graphbin/

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / graphbin


Commits:
6ca9f9e4 by Shayan Doust at 2020-07-15T18:09:05+01:00
Patch to change python files that graphbin invokes to the ones under /usr/share/graphbin/

- - - - -


2 changed files:

- + debian/patches/change_python_script_paths.patch
- + debian/patches/series


Changes:

=====================================
debian/patches/change_python_script_paths.patch
=====================================
@@ -0,0 +1,62 @@
+Description: change python script invoke locations of graphbin.py
+ graphbin.py expects the scripts to be under src/. We install these python files into /usr/share/graphbin/ instead.
+Author: Shayan Doust <hello at shayandoust.me>
+Last-Update: 2020-07-15
+---
+
+--- graphbin.orig/graphbin.py
++++ graphbin/graphbin.py
+@@ -143,7 +143,7 @@
+ # Run GraphBin
+ #---------------------------------------------------
+ if assembler.lower() == "spades":
+-    cmdGraphBin = """python "{0}src/graphbin_SPAdes.py" --graph "{1}" --paths "{2}" --binned "{3}" --output "{4}" --prefix "{5}" --max_iteration "{6}" --diff_threshold "{7}" """.format(
++    cmdGraphBin = """python3 "/usr/share/graphbin/graphbin_SPAdes.py" --graph "{1}" --paths "{2}" --binned "{3}" --output "{4}" --prefix "{5}" --max_iteration "{6}" --diff_threshold "{7}" """.format(
+         os.path.dirname(__file__), 
+         assembly_graph_file, 
+         contig_paths, 
+@@ -154,7 +154,7 @@
+         diff_threshold)
+ 
+ elif assembler.lower() == "sga":
+-    cmdGraphBin = """python "{0}src/graphbin_SGA.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
++    cmdGraphBin = """python3 "/usr/share/graphbin/graphbin_SGA.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
+         os.path.dirname(__file__), 
+         assembly_graph_file,
+         contig_bins_file, 
+@@ -164,7 +164,7 @@
+         diff_threshold)
+ 
+ elif assembler.lower() == "megahit":
+-    cmdGraphBin = """python "{0}src/graphbin_MEGAHIT.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
++    cmdGraphBin = """python3 "/usr/share/graphbin/graphbin_MEGAHIT.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
+         os.path.dirname(__file__), 
+         assembly_graph_file,
+         contig_bins_file, 
+@@ -174,7 +174,7 @@
+         diff_threshold)
+ 
+ elif assembler.lower() == "flye":
+-    cmdGraphBin = """python "{0}src/graphbin_Flye.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
++    cmdGraphBin = """python3 "/usr/share/graphbin/graphbin_Flye.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
+         os.path.dirname(__file__), 
+         assembly_graph_file,
+         contig_bins_file, 
+@@ -184,7 +184,7 @@
+         diff_threshold)
+ 
+ elif assembler.lower() == "canu":
+-    cmdGraphBin = """python "{0}src/graphbin_Canu.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
++    cmdGraphBin = """python3 "/usr/share/graphbin/graphbin_Canu.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
+         os.path.dirname(__file__), 
+         assembly_graph_file,
+         contig_bins_file, 
+@@ -194,7 +194,7 @@
+         diff_threshold)
+ 
+ elif assembler.lower() == "miniasm":
+-    cmdGraphBin = """python "{0}src/graphbin_Miniasm.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
++    cmdGraphBin = """python3 "/usr/share/graphbin/graphbin_Miniasm.py" --graph "{1}" --binned "{2}" --output "{3}" --prefix "{4}" --max_iteration "{5}" --diff_threshold "{6}" """.format(
+         os.path.dirname(__file__), 
+         assembly_graph_file,
+         contig_bins_file, 


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+change_python_script_paths.patch



View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/commit/6ca9f9e46fb679c1d57a38e226829556fae01698

-- 
View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/commit/6ca9f9e46fb679c1d57a38e226829556fae01698
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