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newick display: add imagemagick dependency #2710

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Dec 1, 2019
Merged

newick display: add imagemagick dependency #2710

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af65015
newick display: remove png output
bernt-matthias Nov 30, 2019
34929cf
newick: added imagemagick
bernt-matthias Dec 1, 2019
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19 changes: 9 additions & 10 deletions tools/newick_utils/newick_display.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
<tool id="newick_display" name="Newick Display" version="1.6">
<tool id="newick_display" name="Newick Display" version="1.6+galaxy1">
<description>visualize a phylogenetic tree</description>
<edam_operations>
<edam_operation>operation_0567</edam_operation>
</edam_operations>
<requirements>
<requirement type="package" version="1.6">newick_utils</requirement>
<requirement type="package" version="7.0.9_6">imagemagick</requirement>
</requirements>
<command detect_errors="aggressive"><![CDATA[
nw_display
Expand Down Expand Up @@ -36,15 +37,13 @@ nw_display
-w $width
$radial

'$fileNewick' > output.svg

#if $outformat == 'png':
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Is that maybe also due to the bug fixed by galaxyproject/galaxy#9052 ? Because this would just move output.svg '$output' instead of running the conversion ?

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nope. convert was just not installed. The container test output was convert: command not found.

I tried on my local system to use convert and gm convert and both were not able to create a png from the svg.

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I was able to add imagemagick from conda-forge and got a png with this patch:

diff --git a/tools/newick_utils/newick_display.xml b/tools/newick_utils/newick_display.xml
index fbe029b5e..5dcc7b17a 100644
--- a/tools/newick_utils/newick_display.xml
+++ b/tools/newick_utils/newick_display.xml
@@ -5,6 +5,7 @@
     </edam_operations>
     <requirements>
         <requirement type="package" version="1.6">newick_utils</requirement>
+        <requirement type="package" version="7.0.9_6">imagemagick</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 nw_display

But the png seems to miss fonts ?
tree

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@mvdbeek mvdbeek Nov 30, 2019 •
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Cool, we can add a minimal fonts package like this to fix it:

diff --git a/tools/newick_utils/newick_display.xml b/tools/newick_utils/newick_display.xml
index fbe029b5e..c75f8685c 100644
--- a/tools/newick_utils/newick_display.xml
+++ b/tools/newick_utils/newick_display.xml
@@ -5,6 +5,8 @@
     </edam_operations>
     <requirements>
         <requirement type="package" version="1.6">newick_utils</requirement>
+        <requirement type="package" version="7.0.9_6">imagemagick</requirement>
+        <requirement type="package" version="1">fonts-conda-forge</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 nw_display
@@ -110,7 +112,7 @@ nw_display
             <param name="radial" value="-r"/>
             <param name="branchlength" value="true"/>
             <param name="outformat" value="png"/>
-            <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
+            <output name="output" file="tree.png" ftype="png" compare="sim_size" delta="18000"/>
         </test>
          <test><!-- test with txt output format -->
             <param name="fileNewick" value="tree.nwk"/>

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great. woudn't it be better to add the fonts package as a requirement to the imagemagick recipe?

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Possibly, I'm not sure how that decision is made. It seems imagemagick will use whatever is available.

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lets see conda-forge/imagemagick-feedstock#101 .. I will restore the original code.

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out of interest ... does graphicsmagick work?

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gm gives the following error gm convert: invalid primitive argument (small).

&& convert output.svg output.png
&& mv output.png '$output'
#else:
&& mv output.svg '$output'
#end if
'$fileNewick'

#if $outformat == 'png':
| convert - 'png:$output'
#else:
> '$output'
#end if
]]></command>
<inputs>
<param name="fileNewick" format="txt,newick,nw,nwk,nhx,mothur.tre" type="data" label="Newick file"/>
Expand Down Expand Up @@ -112,7 +111,7 @@ nw_display
<param name="outformat" value="png"/>
<output name="output" file="tree.png" ftype="png" compare="sim_size" delta="15000"/>
</test>
<test><!-- test with txt output format -->
<test><!-- test with txt output format -->
<param name="fileNewick" value="tree.nwk"/>
<param name="outformat" value="txt"/>
<output name="output" file="tree.txt" ftype="txt"/>
Expand Down