dear all, I'm trying to install galaxy locally, on a Linux Suse 11 SP1 with python 2.6 and mercurial 2.3.2. I am behind a proxy with user authentication. 1) Get the latest copy from the repository
hg clone https://bitbucket.org/galaxy/galaxy-dist/ cd galaxy-dist hgupdate stable
after initial disconnects due to size of download, it worked well.
2) Start it up
sh run.sh Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/home/galaxy/galaxy-dist/lib/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: mercurial==2.2.3 Fetch failed.
I've modified eggs.ini by modifying mercurial = 2.2.3 with mercurial = 2.3.2 I've then rerun it
sh run.sh Some eggs are out of date, attempting to fetch... Mako 0.4.1 couldn't be downloaded automatically. You can try building it by hand with: python scripts/scramble.py -e Mako Fetch failed.
I've then tried to follow scramble.py procedure however I got even more mistakes perhaps since scramble is using urllib instead of urllib3.
python scripts/scramble.py -e Mako fetch_one(): Trying to fetch: http://eggs.galaxyproject.org/Mako/Mako-0.4.1.tar.gz Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 52, in scramble self.fetch_source() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 112, in fetch_source self.source_path = self.fetch_one( urls ) File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 91, in fetch_one URLRetriever().retrieve( url, file + '.download' ) File "/usr/lib64/python2.6/urllib.py", line 239, in retrieve fp = self.open(url, data) File "/usr/lib64/python2.6/urllib.py", line 207, in open return getattr(self, name)(url) File "/usr/lib64/python2.6/urllib.py", line 346, in open_http h.endheaders() File "/usr/lib64/python2.6/httplib.py", line 908, in endheaders self._send_output() File "/usr/lib64/python2.6/httplib.py", line 780, in _send_output self.send(msg) File "/usr/lib64/python2.6/httplib.py", line 739, in send self.connect() File "/usr/lib64/python2.6/httplib.py", line 720, in connect self.timeout) File "/usr/lib64/python2.6/socket.py", line 547, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): IOError: [Errno socket error] [Errno -2] Name or service not known
Needless to say, that wget worked fine
wget http://eggs.galaxyproject.org/Mako/Mako-0.4.1.tar.gz
However, I realised that it is going to give this same error message for any egg.
I therefore followed the approach of downloading the eggs from a machine directly connected to the internet and it worked.
I was wondering, if you have any plan to modify galaxy and making fetch_eggs supporting also proxy with authentication.
thankyou and compliments. luca