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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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