[med-svn] [Git][med-team/ivar][master] Patch to include local file to avoid lintian warning

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / ivar


Commits:
a05e6ab5 by Pranav Ballaney at 2020-06-17T06:04:02+05:30
Patch to include local file to avoid lintian warning

- - - - -


3 changed files:

- debian/ivar-doc.install
- + patches/fix_pipeline_link.patch
- + patches/series


Changes:

=====================================
debian/ivar-doc.install
=====================================
@@ -1 +1,2 @@
-docs/html      usr/share/doc/ivar
+docs/html               usr/share/doc/ivar
+pipeline/pipeline.png   usr/share/doc/ivar/html/pipeline.png


=====================================
patches/fix_pipeline_link.patch
=====================================
@@ -0,0 +1,11 @@
+--- a/docs/html/cookbookpage.html
++++ b/docs/html/cookbookpage.html
+@@ -73,7 +73,7 @@ $(function() {
+ <p>The two pipelines are distributed along with iVar and are present in the<a 
href="https://github.com/andersen-lab/ivar/tree/master/pipeline";>pipeline/</a> 
and <a 
href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field";>pipeline_field/</a>
 fodlers respectively.</p>
+ <p>For both pipelines, there are four parameters that will have to be set in 
beginning of the Snakefile.</p>
+ <div class="fragment"><div class="line">in_dir = &quot;&lt;input fastq 
files&gt;&quot;</div><div class="line">out_dir = &quot;&lt;output 
directory&gt;&quot;</div><div class="line">bed = 
&quot;&lt;bed-file-with-primer-positions&gt;&quot;</div><div 
class="line">ref=&quot;&lt;path to reference fasta&gt;&quot;</div></div><!-- 
fragment --><div class="image">
+-<img 
src="https://raw.githubusercontent.com/andersen-lab/ivar/master/pipeline/pipeline.png";
 width="500"/>
++<img src="pipeline.png" width="500"/>
+ </div>
+ <h3>Call iSNVs from samples with known reference sequence</h3>
+ <p><a 
href="https://github.com/andersen-lab/paper_2018_primalseq-ivar/blob/master/cookbook/CookBook.ipynb";>Link
 to Jupyter Notebook</a></p>


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



View it on GitLab: 
https://salsa.debian.org/med-team/ivar/-/commit/a05e6ab556eba22a5f86c4b36a4335e4a85cda89

-- 
View it on GitLab: 
https://salsa.debian.org/med-team/ivar/-/commit/a05e6ab556eba22a5f86c4b36a4335e4a85cda89
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