MUMmer -- dependency issue?

[jennaj]

WARNING: Unable to run 'gnuplot /corral4/main/jobs/049/522/49522531/_job_tmp/tmprv90kzfn/ref_qry.gp', Inappropriate ioctl for device
ERROR: PNG file not created.
ERROR: Failed to produce output file(s).

Seems similar to this: mummer4/mummer#36

Tests:

1. test mummerplot_wrapper/0.0.7 mvdbeek/usegalaxy-tests#91
2. https://usegalaxy.org/u/jen-galaxyproject/h/test-mummer-dotplot
3. https://usegalaxy.eu/u/jenj/h/test-mummer-dotplot

[bgruening]

I'm looking at it. The first observation is that tool is using old TS packages as dependencies on EU. So I will try to create a container and conda env.

[bgruening]

The environment is called /usr/local/tools/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a and should contain ghostscript=9.10,mummer=3.23,gnuplot=4.6 for version 0.0.7.

I now get this error with your test-data @jennaj

Reading mummer file /data/jwd03f/main/058/834/58834531/tmp/tmpq6hx3uzl/ref_qry.mums (use mummer -c)
Writing plot files /data/jwd03f/main/058/834/58834531/tmp/tmpq6hx3uzl/ref_qry.fplot, /data/jwd03f/main/058/834/58834531/tmp/tmpq6hx3uzl/ref_qry.rplot
ERROR: No alignment data to plot

With the tool test data I get now this:

WARNING: Unable to run 'gnuplot /data/jwd03f/main/058/834/58834539/tmp/tmpsp0htaqq/ref_qry.gp', Inappropriate ioctl for device
Reading mummer file /data/jwd03f/main/058/834/58834539/tmp/tmpsp0htaqq/ref_qry.mums (use mummer -c)
Writing plot files /data/jwd03f/main/058/834/58834539/tmp/tmpsp0htaqq/ref_qry.fplot, /data/jwd03f/main/058/834/58834539/tmp/tmpsp0htaqq/ref_qry.rplot
Writing gnuplot script /data/jwd03f/main/058/834/58834539/tmp/tmpsp0htaqq/ref_qry.gp
Rendering plot /data/jwd03f/main/058/834/58834539/tmp/tmpsp0htaqq/ref_qry.ps
Can't find PostScript prologue file prologue.ps
	loadpath is empty
	gnuplotrc is read from /anaconda/envs/_build/share/gnuplot/4.6
	no XAPPLRESDIR found in the environment,
	    falling back to "/etc/X11/app-defaults/"
Please copy prologue.ps to one of the above directories
or set the environmental variable GNUPLOT_PS_DIR
or set the loadpath appropriately

So some progress, but not fixed yet.

[bgruening]

The missing file is actually in the env, but the package was build with a wrong path (/anaconda/envs/_build/share/gnuplot/4.6/):

mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a) galaxy@sn06:/usr/local/tools/_conda/envs/mulled-v1-209b1ee7c1ff6bf2472f303b787aac801ab87f50fc6ce1629f953e8dd02b3f3a$ ll share/gnuplot/4.6/PostScript/
total 108
-rw-r--r-- 5 galaxy galaxy  2123 Jan 31  2016 8859-15.ps
-rw-r--r-- 5 galaxy galaxy  2144 Jan 31  2016 8859-1.ps
-rw-r--r-- 5 galaxy galaxy  2344 Jan 31  2016 8859-2.ps
-rw-r--r-- 5 galaxy galaxy  2238 Jan 31  2016 8859-9.ps
-rw-r--r-- 5 galaxy galaxy 37634 Jan 31  2016 aglfn.txt
-rw-r--r-- 5 galaxy galaxy  2187 Jan 31  2016 cp1250.ps
-rw-r--r-- 5 galaxy galaxy  2792 Jan 31  2016 cp1251.ps
-rw-r--r-- 5 galaxy galaxy  2396 Jan 31  2016 cp437.ps
-rw-r--r-- 5 galaxy galaxy  2335 Jan 31  2016 cp850.ps
-rw-r--r-- 5 galaxy galaxy  2110 Jan 31  2016 cp852.ps
-rw-r--r-- 5 galaxy galaxy  2461 Jan 31  2016 koi8r.ps
-rw-r--r-- 5 galaxy galaxy  2281 Jan 31  2016 koi8u.ps
-rw-r--r-- 5 galaxy galaxy 13991 Jan 31  2016 prologue.ps
-rw-r--r-- 5 galaxy galaxy  2776 Jan 31  2016 utf-8.ps
``