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License: GNU Affero General Public License v3.0
Home Page: https://ngphylogeny.fr/
License: GNU Affero General Public License v3.0
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)
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 "ร 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 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)
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