newick display: add imagemagick dependency

[bernt-matthias]

imagemagick requirement was missing anyway. since for some reason
neither imagemagick not graphicsmagick can convert the image I
suggest to stick to svg only for now.

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[mvdbeek]

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 ?

[bernt-matthias]

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.

[mvdbeek]

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 ?

[mvdbeek]

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"/>

[bernt-matthias]

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

[mvdbeek]

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

[bernt-matthias]

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

[bgruening]

out of interest ... does graphicsmagick work?

[bernt-matthias]

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

[mvdbeek]

Cool!