error message from pygenometracks

[diegohernansanchez]

Hi, I was wondering if you could be so kind as to help me with a problem. I freshly installed deeptools and pygenometracks, but I found an error from matplotlib when trying to use the second:

runned pygenometracks

$ pyGenomeTracks --tracks tracks.ini --region SL2.50ch03:66,540,000-66,610,000 --outFileName nice_image_minus.pdf & [1] 13902 diego_test@boeing:~/1_RNAseq_tomato_fig$ [INFO:tracksClass.py:130 - init()] time initializing track(s): [INFO:tracksClass.py:356 - print_elapsed()] 0.00660514831543 [DEBUG:tracksClass.py:161 - plot()] Figure size in cm is 40 x 10. Dpi is set to 72

Traceback (most recent call last): File "/home/diego_test/miniconda2/bin/pyGenomeTracks", line 11, in main(args) File "/home/diego_test/miniconda2/lib/python2.7/site-packages/pygenometracks/plotTracks.py", line 300, in main trp.plot(args.outFileName, *region, title=args.title) File "/home/diego_test/miniconda2/lib/python2.7/site-packages/pygenometracks/tracksClass.py", line 178, in plot track.plot(axis, label_axis, chrom, start, end) File "/home/diego_test/miniconda2/lib/python2.7/site-packages/pygenometracks/tracksClass.py", line 720, in plot ax.axis['x'].axis.set_tick_params(which='minor', bottom='on') File "/home/diego_test/miniconda2/lib/python2.7/site-packages/matplotlib/axis.py", line 856, in set_tick_params kwtrans = self._translate_tick_kw(kw, to_init_kw=True) File "/home/diego_test/miniconda2/lib/python2.7/site-packages/matplotlib/axis.py", line 898, in _translate_tick_kw kwtrans['tick1On'] = _string_to_bool(kw.pop('bottom')) File "/home/diego_test/miniconda2/lib/python2.7/site-packages/matplotlib/cbook/init.py", line 641, in _string_to_bool warn_deprecated("2.2", "Passing one of 'on', 'true', 'off', 'false' as a " File "/home/diego_test/miniconda2/lib/python2.7/site-packages/matplotlib/cbook/deprecation.py", line 107, in warn_deprecated warnings.warn(message, mplDeprecation, stacklevel=1) matplotlib.cbook.deprecation.MatplotlibDeprecationWarning: Passing one of 'on', 'true', 'off', 'false' as a boolean is deprecated; use an actual boolean (True/False) instead.

I suspect this happens due to the installation process. In a fresh Miniconda2 session, I first installed deeptools as: $ conda create --name deeptools deeptools -c conda-forge -c bioconda

I then installed pygenometracks: $ conda install -c bioconda pygenometracks

While doing this, I realized that conda made an update of itself, and after finishing the installation of pygenometracks, deeptools 'dissapeared', and I had to install it afresh: $ conda install -c bioconda deeptools

While doing the re-installation of deeptools, I realized that matplotlib was upgraded to a newer version, whereas pygenometracks was dowgraded to a previous version. The outcome was that the deeptools functions I tried (bamCoverage) works, but the pygenometrack doenst. Find below all the report of the installation process:

diego_test_CONDA.txt

[fidelram]

I am not so sure the problem is related to the installation. I don't even know if this is an error because I only see warnings. Do you obtain any image?

[dpryan79]

At least under python 3.5 pyGenomeTracks 2.0, hicExplorer 2.0, and deepTools 3.0.2 install happily in the same environment without any downgrading of anything.

[vivekbhr]

@diegohernansanchez Not sure why there's dependency issue but you can try installing pyGenomeTracks along with HiCExplorer in its own env to check if that fixes your issue.

conda create -n pyGenomeTracks -c bioconda pyGenomeTracks

[diegohernansanchez]

I first tried standard re-installing of pyGenomeTracks and now it works.

$ conda install -c bioconda pygenometracks

Thank you very much guys for your feedback, sorry for the inconvenience. Best diego

On 16/05/2018 07:34, Vivek Bhardwaj wrote:

Not sure why there's dependency issue but you can try installing pyGenomeTracks along with HiCExplorer in its own env to check if that fixes your issue.

|conda create -n pyGenomeTracks -c bioconda pyGenomeTracks|

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-- Diego H. Sanchez, PhD IFEVA (CONICET-UBA), Facultad de Agronomia (FAUBA) Universidad de Buenos Aires (UBA) Av. San Martín 4453 C1417DSE Buenos Aires Argentina

Email: diegosanchez@agro.uba.ar Tel: +54-11-528-70127