[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 = "<input fastq files>"</div><div class="line">out_dir = "<output directory>"</div><div class="line">bed = "<bed-file-with-primer-positions>"</div><div class="line">ref="<path to reference fasta>"</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

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