c3bi-pasteur-fr / ngphylogeny-django Goto Github PK

Hi there

I'm not sure this is the right place to post, but I used the "contact" form of ngphylogeny.fr and never got any answer.

I regularly get some "Error 500" when I use ngphylogeny.fr especially when I try to use the "à la carte" workflow.
I cannot have a working workflow with MUSCLE or Clustal Omega, only MAFFT (and not all the time).
I randomly also have "Error 500" with the one click workflow

Thank you for you help.

I tried installing ngphylogeny a few days ago and I got into some trouble with dependencies listed in the requirement.txt file. Indeed, Python will install the latest version of python-slugify and bibtexparser, which both raise a lot of errors (at different stages of the installation) because newer versions of these packages no longer support Python 2.7.

Here is a quick patch if you are interested in updating the README and Python setup files:

diff --git a/requirement.txt b/requirement.txt
index 5e2bda7..125464a 100644
--- a/requirement.txt
+++ b/requirement.txt
@@ -4,8 +4,8 @@ django-crispy-forms==1.6
 bioblend==0.10
 django-markdown-deux==1.0.5
 biopython==1.70
-python-slugify
-bibtexparser
+python-slugify==1.2.6
+bibtexparser==0.6.2
 celery[redis]
 uwsgi
 django-simple-captcha

I should note I wasn't able to proceed further beyond linking the Django app to our Galaxy server running on a local machine. When it came to import existing tools from Galaxy to the Django app, I got the error shown below:

No result was found for query  phylogeny
CommandError: Tool BMGE is not imported, and cannot be associated to Alignment Curation,Tool display in OneClick Workflows,Tool display in Advanced Workflows,Tool display in Workflow Maker flag(s)

I get this error when trying to import tools:

(python manage.py importtools --galaxyurl=http://localhost:8080/ --query="phylogeny" --flags=toolflags.txt --inputfields=toolfields.txt
Startup Code
Traceback (most recent call last):
File "manage.py", line 10, in
execute_from_command_line(sys.argv)
File "/Users/agharrab/anaconda2/envs/ngphylo/lib/python2.7/site-packages/django/core/management/init.py", line 364, in execute_from_command_line
utility.execute()
File "/Users/agharrab/anaconda2/envs/ngphylo/lib/python2.7/site-packages/django/core/management/init.py", line 356, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/Users/agharrab/anaconda2/envs/ngphylo/lib/python2.7/site-packages/django/core/management/base.py", line 283, in run_from_argv
self.execute(*args, **cmd_options)
File "/Users/agharrab/anaconda2/envs/ngphylo/lib/python2.7/site-packages/django/core/management/base.py", line 330, in execute
output = self.handle(*args, **options)
File "/Users/agharrab/PycharmProjects/ngphylogeny-django-master/tools/management/commands/importtools.py", line 57, in handle
self.import_tools(galaxy_url, query, tool_id, force)
File "/Users/agharrab/PycharmProjects/ngphylogeny-django-master/tools/management/commands/importtools.py", line 88, in import_tools
for tool in tools_list:
UnboundLocalError: local variable 'tools_list' referenced before assignment)