No PDF document generated

[SMorrison42]

Welcome to the pyGenomeTracks GitHub repository! Before opening the issue please check
that the following requirements are met :

• Search whether this issue (or a similar issue) has been solved before
  using the search tab above. Link the previous issue if appropriate below.

• Paste your pyGenomeTracks version (pyGenomeTracks --version) and your python
  version (python --version) below.

pyGenomeTracks verison 3.5

python version 3.7

• Paste the full pyGenomeTracks command that produces the issue below
  (ignore if you simply spotted the issue in the code/documentation).
  pyGenomeTracks --tracks tracks.ini --BED test.bed -o test.pdf

• Paste the output printed on screen from the command that produces the issue
  below (ignore if you simply spotted the issue in the code/documentation).
  INFO:pygenometracks.tracksClass:initialize 1. [x-axis]
  INFO:pygenometracks.tracksClass:initialize 2. [spacer]
  INFO:pygenometracks.tracksClass:initialize 3. [test]

No PDF file is generated after the pyGenomeTracks command is generated

[lldelisle]

Hi,
Thanks for the report.
It may be that bedtools is not accessible in your environment like in #273
If bedtools was accessible, please could you give more details on the ini file and the file in the [test] section?

[yanchunzhang]

Hi,
Thanks for the report.
It may be that bedtools is not accessible in your environment like in #273
If bedtools was accessible, please could you give more details on the ini file and the file in the [test] section?

This is very helpful! I got the same problem and was a little disappointed until I saw this answer. Could you please tell users to load bedtools in their environment before running pyGenomeTracks in your documentation or tutorial page? I think that'll help other users like me and the questioner.

[lldelisle]

It will be solved in the next version:
You would have a message:
"It seems that BEDTools is not installed. Cannot subset the file." I can also add it to the documentation.

[lldelisle]

Hi,
The new version 3.5.1 takes care of this.