[med-svn] [paleomix] 03/04: Point to local installed kronatools (in package radiant)
Andreas Tille
tille at debian.org
Tue Feb 14 15:37:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository paleomix.
commit c9e7072add617231dcdf8fda2598d4a5c88ad763
Author: Andreas Tille <tille at debian.org>
Date: Tue Feb 14 16:12:33 2017 +0100
Point to local installed kronatools (in package radiant)
---
debian/control | 1 +
debian/patches/avoid_privacy_breach.patch | 73 +++++++++++++++++++++++++++++++
debian/patches/series | 1 +
3 files changed, 75 insertions(+)
diff --git a/debian/control b/debian/control
index 2d6e5fc..fdba2ed 100644
--- a/debian/control
+++ b/debian/control
@@ -32,6 +32,7 @@ Depends: ${misc:Depends},
mapdamage,
phylip,
picard-tools,
+ radiant,
raxml,
samtools
Suggests: examl
diff --git a/debian/patches/avoid_privacy_breach.patch b/debian/patches/avoid_privacy_breach.patch
new file mode 100644
index 0000000..d6faec7
--- /dev/null
+++ b/debian/patches/avoid_privacy_breach.patch
@@ -0,0 +1,73 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 14 Feb 2017 12:04:19 +0100
+Description: Point to local installed kronatools (in package radiant)
+
+--- a/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_M.0182896.all.html
++++ b/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_M.0182896.all.html
+@@ -2,14 +2,14 @@
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+ <meta charset="utf-8"/>
+- <link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
+- <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>
+- <script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
++ <link rel="shortcut icon" href="file:///usr/share/perl5/KronaTools/img/favicon.ico"/>
++ <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from kronatools - please install radiant package."}</script>
++ <script src="file:///usr/share/perl5/KronaTools/src/krona-2.0.js"></script>
+ </head>
+ <body>
+- <img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
+- <img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
+- <img id="logo" src="http://krona.sourceforge.net/img/logo.png" style="display:none"/>
++ <img id="hiddenImage" src="file:///usr/share/perl5/KronaTools/img/img/hidden.png" style="display:none"/>
++ <img id="loadingImage" src="file:///usr/share/perl5/KronaTools/img/loading.uri" style="display:none"/>
++ <img id="logo" src="file:///usr/share/perl5/KronaTools/img/logo.png" style="display:none"/>
+ <noscript>Javascript must be enabled to view this page.</noscript>
+ <div style="display:none">
+ <krona collapse="true" key="true">
+--- a/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1845A.all.html
++++ b/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1845A.all.html
+@@ -2,14 +2,14 @@
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+ <meta charset="utf-8"/>
+- <link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
+- <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>
+- <script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
++ <link rel="shortcut icon" href="file:///usr/share/perl5/KronaTools/img/favicon.ico"/>
++ <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from kronatools - please install radiant package."}</script>
++ <script src="file:///usr/share/perl5/KronaTools/src/krona-2.0.js"></script>
+ </head>
+ <body>
+- <img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
+- <img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
+- <img id="logo" src="http://krona.sourceforge.net/img/logo.png" style="display:none"/>
++ <img id="hiddenImage" src="file:///usr/share/perl5/KronaTools/img/img/hidden.png" style="display:none"/>
++ <img id="loadingImage" src="file:///usr/share/perl5/KronaTools/img/loading.uri" style="display:none"/>
++ <img id="logo" src="file:///usr/share/perl5/KronaTools/img/logo.png" style="display:none"/>
+ <noscript>Javascript must be enabled to view this page.</noscript>
+ <div style="display:none">
+ <krona collapse="true" key="true">
+--- a/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1889.all.html
++++ b/paleomix/resources/examples/nature_protocols/example_results/profiling/krona/Figure_Krona_Pi1889.all.html
+@@ -2,14 +2,14 @@
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+ <head>
+ <meta charset="utf-8"/>
+- <link rel="shortcut icon" href="http://krona.sourceforge.net/img/favicon.ico"/>
+- <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from \"http://krona.sourceforge.net\"."}</script>
+- <script src="http://krona.sourceforge.net/src/krona-2.0.js"></script>
++ <link rel="shortcut icon" href="file:///usr/share/perl5/KronaTools/img/favicon.ico"/>
++ <script id="notfound">window.onload=function(){document.body.innerHTML="Could not get resources from kronatools - please install radiant package."}</script>
++ <script src="file:///usr/share/perl5/KronaTools/src/krona-2.0.js"></script>
+ </head>
+ <body>
+- <img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" style="display:none"/>
+- <img id="loadingImage" src="http://krona.sourceforge.net/img/loading.gif" style="display:none"/>
+- <img id="logo" src="http://krona.sourceforge.net/img/logo.png" style="display:none"/>
++ <img id="hiddenImage" src="file:///usr/share/perl5/KronaTools/img/img/hidden.png" style="display:none"/>
++ <img id="loadingImage" src="file:///usr/share/perl5/KronaTools/img/loading.uri" style="display:none"/>
++ <img id="logo" src="file:///usr/share/perl5/KronaTools/img/logo.png" style="display:none"/>
+ <noscript>Javascript must be enabled to view this page.</noscript>
+ <div style="display:none">
+ <krona collapse="true" key="true">
diff --git a/debian/patches/series b/debian/patches/series
index c186495..19b90b2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
avoid_downloading_prerequisites.patch
fix_makefile_test.patch
work_around_os.getlogin.patch
+avoid_privacy_breach.patch
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