I've been trying to track down why I can't get anything from the toolshed installed and finally have it figured out. Whenever I tried to install anything I always got an Error with no explanation of what the error was. After enabling Debug messages into the log file, I see the error is: tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning repository: httpsconnection instance has no attribute '_set_hostport' I googled around and found out this is a known bug/issue with older version of Mercurial and was fixed in v3. I added a line to hg_util.py to see where it picks up hg. Its using version 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. I have the newest version of mercurial installed in my site-packages folder but I guess that's not what galaxy wants. So my question is, how do I get Galaxy to use the latest version of Mercurial? And, Why did it download an older version? ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Thanks. Is there an alternative way I can install tools from the Toolshed? This problem pretty much renders the toolshed unusable for me... On Mon, Jan 5, 2015 at 11:14 AM, John Chilton <jmchilton(a)gmail.com&gt; wrote: > It is certainly the case that Galaxy should be using the latest > version of mercurial given a number of high profile bugs with older > versions. Unfortunately it doesn't seem possible to just drop the new > version it - there are some API changes that prevent Galaxy from > loading when doing this and the number of people who can add new eggs > to Galaxy is low. > > I have created a Trello card to track this issue: > > https://trello.com/c/9A9uIav0 > > Let us know if you happen to find a workaround for this issue. > > -John > > > On Mon, Dec 22, 2014 at 2:55 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; > wrote: >> I've been trying to track down why I can't get anything from the toolshed >> installed and finally have it figured out. >> >> Whenever I tried to install anything I always got an Error with no >> explanation of what the error was. After enabling Debug messages into > the >> log file, I see the error is: >> >> tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning >> repository: httpsconnection instance has no attribute '_set_hostport' >> >> I googled around and found out this is a known bug/issue with older > version >> of Mercurial and was fixed in v3. >> >> I added a line to hg_util.py to see where it picks up hg. Its using > version >> 2.2.3. Indeed, one of the eggs downloaded by Galaxy is mercurial-2.2.3. >> >> I have the newest version of mercurial installed in my site-packages > folder >> but I guess that's not what galaxy wants. So my question is, how do I > get >> Galaxy to use the latest version of Mercurial? And, Why did it download > an >> older version? >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Yes, I think I found the root cause...its because the Galaxy egg for mercurial is using an older version of Mercurial that has this known bug. The only real fix is to upgrade the Galaxy egg to mercurial 3.x. The only way I know of to test this is to build a new Galaxy egg which I'm not familiar with. But as I understand it the new Mercurial version will also break Galaxy. On Mon, Jan 5, 2015 at 6:19 PM, Björn Grüning <bjoern.gruening(a)gmail.com&gt; wrote: > > Hi Ryan, > > unfortunately not (yet). But I'm really surprised you are getting this > error. It working for me and in our docker containers and other > deployments. Can we try to detect the root cause of this error? Do you > have conflicting mercurial version. > > Cheers, > Bjoern > > > Thanks. Is there an alternative way I can install tools from the > > Toolshed? This problem pretty much renders the toolshed unusable for > > me... > > > > On Mon, Jan 5, 2015 at 11:14 AM, John Chilton <jmchilton(a)gmail.com&gt; > > wrote: > > > >> It is certainly the case that Galaxy should be using the latest > >> version of mercurial given a number of high profile bugs with older > >> versions. Unfortunately it doesn't seem possible to just drop the new > >> version it - there are some API changes that prevent Galaxy from > >> loading when doing this and the number of people who can add new eggs > >> to Galaxy is low. > >> > >> I have created a Trello card to track this issue: > >> > >> https://trello.com/c/9A9uIav0 > >> > >> Let us know if you happen to find a workaround for this issue. > >> > >> -John > >> > >> > >> On Mon, Dec 22, 2014 at 2:55 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; > >> wrote: > >>> I've been trying to track down why I can't get anything from the > >>> toolshed > >>> installed and finally have it figured out. > >>> > >>> Whenever I tried to install anything I always got an Error with no > >>> explanation of what the error was. After enabling Debug messages into > >> the > >>> log file, I see the error is: > >>> > >>> tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning > >>> repository: httpsconnection instance has no attribute '_set_hostport' > >>> > >>> I googled around and found out this is a known bug/issue with older > >> version > >>> of Mercurial and was fixed in v3. > >>> > >>> I added a line to hg_util.py to see where it picks up hg. Its using > >> version > >>> 2.2.3. Indeed, one of the eggs downloaded by Galaxy is > >>> mercurial-2.2.3. > >>> > >>> I have the newest version of mercurial installed in my site-packages > >> folder > >>> but I guess that's not what galaxy wants. So my question is, how do I > >> get > >>> Galaxy to use the latest version of Mercurial? And, Why did it > >>> download > >> an > >>> older version? > >>> > >>> ___________________________________________________________ > >>> Please keep all replies on the list by using "reply all" > >>> in your mail client. To manage your subscriptions to this > >>> and other Galaxy lists, please use the interface at: > >>> https://lists.galaxyproject.org/ > >>> > >>> To search Galaxy mailing lists use the unified search at: > >>> http://galaxyproject.org/search/mailinglists/ > >> > > > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > >

Yes, I will look at this this week. I'm using a clean copy of galaxy-dist and will apply against that to see how it works. Thanks a bunch Dave B for doing this! On Thu, Jan 8, 2015 at 9:42 AM, John Chilton <jmchilton(a)gmail.com&gt; wrote: > Hey Ryan, > > It looks like Dave B. has come to rescue with an egg and a patch that > implements this: > > > https://bitbucket.org/galaxy/galaxy-central/pull-request/626/upgrade-merc... > > It probably won't be back-ported to the forthcoming January release > but I would suspect the raw patch > ( > https://api.bitbucket.org/2.0/repositories/galaxy/galaxy-central/diff/dav... > ) > will apply cleanly against the last few releases. If you have some > time and want to apply it to your release and let us know if it fixes > your problems that would probably help the pull request along. > > -John > > On Wed, Jan 7, 2015 at 10:56 AM, Ryan G <ngsbioinformatics(a)gmail.com&gt; > wrote: > > Yes, I think I found the root cause...its because the Galaxy egg for > > mercurial is using an older version of Mercurial that has this known > bug. > > The only real fix is to upgrade the Galaxy egg to mercurial 3.x. > > > > The only way I know of to test this is to build a new Galaxy egg which > I'm > > not familiar with. But as I understand it the new Mercurial version > will > > also break Galaxy. > > > > > > On Mon, Jan 5, 2015 at 6:19 PM, Björn Grüning < > bjoern.gruening(a)gmail.com&gt; > > wrote: > >> > >> Hi Ryan, > >> > >> unfortunately not (yet). But I'm really surprised you are getting this > >> error. It working for me and in our docker containers and other > >> deployments. Can we try to detect the root cause of this error? Do you > >> have conflicting mercurial version. > >> > >> Cheers, > >> Bjoern > >> > >> > Thanks. Is there an alternative way I can install tools from the > >> > Toolshed? This problem pretty much renders the toolshed unusable for > >> > me... > >> > > >> > On Mon, Jan 5, 2015 at 11:14 AM, John Chilton <jmchilton(a)gmail.com&gt; > >> > wrote: > >> > > >> >> It is certainly the case that Galaxy should be using the latest > >> >> version of mercurial given a number of high profile bugs with older > >> >> versions. Unfortunately it doesn't seem possible to just drop the > new > >> >> version it - there are some API changes that prevent Galaxy from > >> >> loading when doing this and the number of people who can add new > eggs > >> >> to Galaxy is low. > >> >> > >> >> I have created a Trello card to track this issue: > >> >> > >> >> https://trello.com/c/9A9uIav0 > >> >> > >> >> Let us know if you happen to find a workaround for this issue. > >> >> > >> >> -John > >> >> > >> >> > >> >> On Mon, Dec 22, 2014 at 2:55 PM, Ryan G < > ngsbioinformatics(a)gmail.com&gt; > >> >> wrote: > >> >>> I've been trying to track down why I can't get anything from the > >> >>> toolshed > >> >>> installed and finally have it figured out. > >> >>> > >> >>> Whenever I tried to install anything I always got an Error with no > >> >>> explanation of what the error was. After enabling Debug messages > into > >> >> the > >> >>> log file, I see the error is: > >> >>> > >> >>> tool_shed.util.hg_util DEBUG 2014-12-22 14:47:48,910 Error cloning > >> >>> repository: httpsconnection instance has no attribute > '_set_hostport' > >> >>> > >> >>> I googled around and found out this is a known bug/issue with older > >> >> version > >> >>> of Mercurial and was fixed in v3. > >> >>> > >> >>> I added a line to hg_util.py to see where it picks up hg. Its > using > >> >> version > >> >>> 2.2.3. Indeed, one of the eggs downloaded by Galaxy is > >> >>> mercurial-2.2.3. > >> >>> > >> >>> I have the newest version of mercurial installed in my > site-packages > >> >> folder > >> >>> but I guess that's not what galaxy wants. So my question is, how > do I > >> >> get > >> >>> Galaxy to use the latest version of Mercurial? And, Why did it > >> >>> download > >> >> an > >> >>> older version? > >> >>> > >> >>> ___________________________________________________________ > >> >>> Please keep all replies on the list by using "reply all" > >> >>> in your mail client. To manage your subscriptions to this > >> >>> and other Galaxy lists, please use the interface at: > >> >>> https://lists.galaxyproject.org/ > >> >>> > >> >>> To search Galaxy mailing lists use the unified search at: > >> >>> http://galaxyproject.org/search/mailinglists/ > >> >> > >> > > >> > > >> > > >> > ___________________________________________________________ > >> > Please keep all replies on the list by using "reply all" > >> > in your mail client. To manage your subscriptions to this > >> > and other Galaxy lists, please use the interface at: > >> > https://lists.galaxyproject.org/ > >> > > >> > To search Galaxy mailing lists use the unified search at: > >> > http://galaxyproject.org/search/mailinglists/ > >> > > > > > >