[med-svn] [metabit] 02/02: Use Debian packaged lefse

[Andreas Tille]

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tille pushed a commit to branch master
in repository metabit.

commit 2434cc9acd220c30d01c6e528fe218bf47dc7c98
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 28 13:58:55 2016 +0200

    Use Debian packaged lefse
---
 debian/patches/debian_packaged_lefse.patch | 53 ++++++++++++++++++++++++++++++
 debian/patches/series                      |  1 +
 2 files changed, 54 insertions(+)

diff --git a/debian/patches/debian_packaged_lefse.patch b/debian/patches/debian_packaged_lefse.patch
new file mode 100644
index 0000000..fab08f2
--- /dev/null
+++ b/debian/patches/debian_packaged_lefse.patch
@@ -0,0 +1,53 @@
+--- a/config.py
++++ b/config.py
+@@ -97,7 +97,7 @@ def _run_config_parser(argv):
+                                                                 is_path=True),
+                      help = "Path to the folder containing metaphlan(2).py and " \
+                      "the database [%default]")
+-    group.add_option("--lefse-path", default = PerHostValue("~/install/lefse",
++    group.add_option("--lefse-path", default = PerHostValue("/usr/bin",
+                                                             is_path = True),
+                      help = "Path to the LEfSe executables [%default] "
+                      "(https://bitbucket.org/nsegata/lefse, "
+--- a/parts.py
++++ b/parts.py
+@@ -354,14 +354,14 @@ def analyzing(makefile, config, metaphla
+         format_options.update(makefile["Lefse"]["format_input"])
+ 
+         format_input_node = SimpleExecNode(os.path.join(config.lefse_path,
+-                                                        "format_input.py"),
++                                                        "format_input"),
+                                            pre_lefse_input,
+                                            run_lefse_input,
+                                            options = format_options,
+                                            subnodes = metaphlan2lefse_node)
+         
+         run_lefse_output = run_lefse_input.replace('lefse.in', 'lefse.out')
+-        run_lefse_node = SimpleExecNode(os.path.join(config.lefse_path, "run_lefse.py"),
++        run_lefse_node = SimpleExecNode(os.path.join(config.lefse_path, "run_lefse"),
+                                   run_lefse_input,
+                                   run_lefse_output,
+                                   makefile["Lefse"]["run_lefse"],
+@@ -372,19 +372,19 @@ def analyzing(makefile, config, metaphla
+             if not makefile['Lefse'][step].has_key('--format'):
+                 makefile['Lefse'][step]['--format'] = fmt
+ 
+-        plot_res_node = SimpleExecNode(os.path.join(config.lefse_path, "plot_res.py"),
++        plot_res_node = SimpleExecNode(os.path.join(config.lefse_path, "plot_res"),
+                                   run_lefse_output,
+                                   run_lefse_output.replace('lefse.out', 'lefse.plot_res.'+fmt),
+                                   makefile["Lefse"]["plot_res"],
+                                   subnodes = run_lefse_node)
+-        plot_clad_node = SimpleExecNode(os.path.join(config.lefse_path, "plot_cladogram.py"),
++        plot_clad_node = SimpleExecNode(os.path.join(config.lefse_path, "plot_cladogram"),
+                                   run_lefse_output,
+                                   run_lefse_output.replace('lefse.out','lefse.cladogram.'+fmt),
+                                   makefile["Lefse"]["plot_cladogram"],
+                                   subnodes = run_lefse_node)
+ 
+         plot_features_obj = ExecNode.customize(os.path.join(config.lefse_path,
+-                                                            "plot_features.py"),
++                                                            "plot_features"),
+                                                #description="Lefse: plot_features",
+                                                subnodes = (metaphlan2lefse_node,
+                                                            run_lefse_node))
diff --git a/debian/patches/series b/debian/patches/series
index fdd23d8..dba726e 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ use_debian_packaged_yaml.patch
 safely_detect_metaphlan.patch
 jar_root.patch
 debian_packaged_picard_tools.patch
+debian_packaged_lefse.patch

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