Re: [galaxy-dev] problems installing tool dependency
Nate, I apologize for taking so long to get back to you but I finally revisited this today. I am on the latest Galaxy version (updated this morning) and am still having trouble getting this installed. Is there a way to force an update on the tool shed that I may be missing? The latest update for Genome Diversity in my tool shed is showing revision 38 (2014-02-28). Once the install fails, I go to the Genome Diversity repository and click Get Repository Updates (under Repository actions) but it says the repository is current and there are no updates available. Sorry these are most likely basic Galaxy questions but we haven’t had a problem installing from the tool shed before. Thank you in advance for your help. Dori From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Tuesday, February 03, 2015 9:50 AM To: Sajdak, Doris Cc: galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu> Subject: Re: [galaxy-dev] problems installing tool dependency Hi Doris, The repository was updated in October with the fix for the dependency path. Please let us know if this fixes it for you. --nate On Mon, Feb 2, 2015 at 1:52 PM, Sajdak, Doris mailto:dj...@buffalo.edu>> wrote: I’m still in a holding pattern on these Miller Lab tools. Has anyone responded to your requests from back in September? I emailed them in August as well and heard nothing. We have users at our university that want to use these tools on our Galaxy instance. If there is no way to get them to change it in the tool shed, is there a way I can install quicktree myself and then tell Galaxy the dependency is installed for the other Miller Lab tools? Thank you for any help you can provide. From: Nate Coraor [mailto:n...@bx.psu.edu<mailto:n...@bx.psu.edu>] Sent: Wednesday, September 24, 2014 2:58 PM To: Will Holtz Cc: Sajdak, Doris; galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu> Subject: Re: [galaxy-dev] problems installing tool dependency I've just looked at this as well, it appears that /pub4 is not exposed and does not allow you to change into it, but it does allow you to fetch if you request files under it via the full path. e.g.: nate@victory% ncftp ftp.sanger.ac.uk<http://ftp.sanger.ac.uk> ... Logged in to ftp.sanger.ac.uk<http://ftp.sanger.ac.uk>. ncftp / > ls ls-lR.gz.ok_to_rsyncREADME .request-for-update.lock .messagepub/ .request-for-update ncftp / > cd pub4 Could not chdir to pub4: server said: pub4: No such file or directory ncftp / > cd /pub4 Could not chdir to /pub4: server said: pub4: No such file or directory ncftp / > get /pub4/resources/software/quicktree/quicktree.tar.gz quicktree.tar.gz: 38.12 kB 124.19 kB/s ncftp / > I'll contact some folks in the Miller Lab to see if the tool can be updated to the path under /pub. On Wed, Sep 24, 2014 at 2:09 PM, Will Holtz mailto:who...@lygos.com>> wrote: I also was able to download quicktree.tar.gz by clicking on the URL in your message. However, when I manually ftp into ftp.sanger.ac.uk<http://ftp.sanger.ac.uk>, there is no /pub4 directory. I'm a bit confused about how those two statements are both true, but maybe it will help someone else figure this out. Removing the '4' does result in a valid path (ftp://ftp.sanger.ac.uk/pub/resources/software/quicktree/quicktree.tar.gz). -Will On Wed, Sep 24, 2014 at 10:57 AM, Sajdak, Doris mailto:dj...@buffalo.edu>> wrote: Hi all, I am trying to install the Genome Diversity tools from the Miller Lab that are in the Galaxy toolshed. I’ve been able to get all dependencies installed except Quicktree. Whenever I try to install it, I get the error: Error downloading from URL ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz: This is the tool_dependencies.xml file for installing quicktree: ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz make quicktree cp -R bin $INSTALL_DIR $INSTALL_DIR/bin I know this is not their file I’m downloading but the thing is, if I copy and paste the URL, I can download it with no problem. I’m not sure why it’s reporting that it can’t be found but the xml looks right to me. I’ve tried contacting the Miller Lab about this but haven’t heard from anyone so I’m hoping someone here can tell me how to move past this problem. Is there a way to install this tool manually and have the main Genome Diversity tools recognize it on the Galaxy server? Also, I noticed when looking at the Tool Dependency Definitions at https://toolshed.g2.bx.psu.edu/ there are errors going back many versions for this tool (see Test r
Re: [galaxy-dev] problems installing tool dependency
I updated Galaxy yesterday and tried the install again but it failed. I may need to do something with updating the repository still though. I’ll try again. Thanks for the help! Dori From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Tuesday, February 03, 2015 9:50 AM To: Sajdak, Doris Cc: galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] problems installing tool dependency Hi Doris, The repository was updated in October with the fix for the dependency path. Please let us know if this fixes it for you. --nate On Mon, Feb 2, 2015 at 1:52 PM, Sajdak, Doris mailto:dj...@buffalo.edu>> wrote: I’m still in a holding pattern on these Miller Lab tools. Has anyone responded to your requests from back in September? I emailed them in August as well and heard nothing. We have users at our university that want to use these tools on our Galaxy instance. If there is no way to get them to change it in the tool shed, is there a way I can install quicktree myself and then tell Galaxy the dependency is installed for the other Miller Lab tools? Thank you for any help you can provide. From: Nate Coraor [mailto:n...@bx.psu.edu<mailto:n...@bx.psu.edu>] Sent: Wednesday, September 24, 2014 2:58 PM To: Will Holtz Cc: Sajdak, Doris; galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu> Subject: Re: [galaxy-dev] problems installing tool dependency I've just looked at this as well, it appears that /pub4 is not exposed and does not allow you to change into it, but it does allow you to fetch if you request files under it via the full path. e.g.: nate@victory% ncftp ftp.sanger.ac.uk<http://ftp.sanger.ac.uk> ... Logged in to ftp.sanger.ac.uk<http://ftp.sanger.ac.uk>. ncftp / > ls ls-lR.gz.ok_to_rsyncREADME .request-for-update.lock .messagepub/ .request-for-update ncftp / > cd pub4 Could not chdir to pub4: server said: pub4: No such file or directory ncftp / > cd /pub4 Could not chdir to /pub4: server said: pub4: No such file or directory ncftp / > get /pub4/resources/software/quicktree/quicktree.tar.gz quicktree.tar.gz: 38.12 kB 124.19 kB/s ncftp / > I'll contact some folks in the Miller Lab to see if the tool can be updated to the path under /pub. On Wed, Sep 24, 2014 at 2:09 PM, Will Holtz mailto:who...@lygos.com>> wrote: I also was able to download quicktree.tar.gz by clicking on the URL in your message. However, when I manually ftp into ftp.sanger.ac.uk<http://ftp.sanger.ac.uk>, there is no /pub4 directory. I'm a bit confused about how those two statements are both true, but maybe it will help someone else figure this out. Removing the '4' does result in a valid path (ftp://ftp.sanger.ac.uk/pub/resources/software/quicktree/quicktree.tar.gz). -Will On Wed, Sep 24, 2014 at 10:57 AM, Sajdak, Doris mailto:dj...@buffalo.edu>> wrote: Hi all, I am trying to install the Genome Diversity tools from the Miller Lab that are in the Galaxy toolshed. I’ve been able to get all dependencies installed except Quicktree. Whenever I try to install it, I get the error: Error downloading from URL ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz: This is the tool_dependencies.xml file for installing quicktree: ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz make quicktree cp -R bin $INSTALL_DIR $INSTALL_DIR/bin I know this is not their file I’m downloading but the thing is, if I copy and paste the URL, I can download it with no problem. I’m not sure why it’s reporting that it can’t be found but the xml looks right to me. I’ve tried contacting the Miller Lab about this but haven’t heard from anyone so I’m hoping someone here can tell me how to move past this problem. Is there a way to install this tool manually and have the main Genome Diversity tools recognize it on the Galaxy server? Also, I noticed when looking at the Tool Dependency Definitions at https://toolshed.g2.bx.psu.edu/ there are errors going back many versions for this tool (see Test runs – Installation errors – Tool dependencies). Thank you for any help you can provide. Dori ** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu ** ___ 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 interfac
Re: [galaxy-dev] problems installing tool dependency
Hi Doris, The repository was updated in October with the fix for the dependency path. Please let us know if this fixes it for you. --nate On Mon, Feb 2, 2015 at 1:52 PM, Sajdak, Doris wrote: > I’m still in a holding pattern on these Miller Lab tools. Has anyone > responded to your requests from back in September? I emailed them in > August as well and heard nothing. We have users at our university that > want to use these tools on our Galaxy instance. If there is no way to get > them to change it in the tool shed, is there a way I can install quicktree > myself and then tell Galaxy the dependency is installed for the other > Miller Lab tools? > > > > Thank you for any help you can provide. > > > > *From:* Nate Coraor [mailto:n...@bx.psu.edu] > *Sent:* Wednesday, September 24, 2014 2:58 PM > *To:* Will Holtz > *Cc:* Sajdak, Doris; galaxy-...@lists.bx.psu.edu > *Subject:* Re: [galaxy-dev] problems installing tool dependency > > > > I've just looked at this as well, it appears that /pub4 is not exposed and > does not allow you to change into it, but it does allow you to fetch if you > request files under it via the full path. > > > > e.g.: > > > > nate@victory% ncftp ftp.sanger.ac.uk > > ... > > Logged in to ftp.sanger.ac.uk. > > ncftp / > ls > > ls-lR.gz.ok_to_rsyncREADME > .request-for-update.lock > > .messagepub/ > .request-for-update > > ncftp / > cd pub4 > > Could not chdir to pub4: server said: pub4: No such file or directory > > ncftp / > cd /pub4 > > Could not chdir to /pub4: server said: pub4: No such file or directory > > ncftp / > get /pub4/resources/software/quicktree/quicktree.tar.gz > > quicktree.tar.gz: 38.12 kB 124.19 > kB/s > > ncftp / > > > > > I'll contact some folks in the Miller Lab to see if the tool can be > updated to the path under /pub. > > > > On Wed, Sep 24, 2014 at 2:09 PM, Will Holtz wrote: > > I also was able to download quicktree.tar.gz by clicking on the URL in > your message. However, when I manually ftp into ftp.sanger.ac.uk, there > is no /pub4 directory. I'm a bit confused about how those two statements > are both true, but maybe it will help someone else figure this out. > Removing the '4' does result in a valid path ( > ftp://ftp.sanger.ac.uk/pub/resources/software/quicktree/quicktree.tar.gz). > > -Will > > > > On Wed, Sep 24, 2014 at 10:57 AM, Sajdak, Doris wrote: > > Hi all, > > > > I am trying to install the Genome Diversity tools from the Miller Lab that > are in the Galaxy toolshed. I’ve been able to get all dependencies > installed except Quicktree. Whenever I try to install it, I get the error: > > > > Error downloading from URL > > ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz: > > > > > > This is the tool_dependencies.xml file for installing quicktree: > > > > > > > > > > > > > > > > target_filename="quicktree_1.1.tar.gz"> > ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz > > > > > > > make quicktree > > > > > > cp -R bin $INSTALL_DIR > > > > > > > >action="prepend_to">$INSTALL_DIR/bin > > > > > > > > > > > > > > > > I know this is not their file I’m downloading but the thing is, if I copy > and paste the URL, I can download it with no problem. I’m not sure why > it’s reporting that it can’t be found but the xml looks right to me. I’ve > tried contacting the Miller Lab about this but haven’t heard from anyone so > I’m hoping someone here can tell me how to move past this problem. Is > there a way to install this tool manually and have the main Genome > Diversity tools recognize it on the Galaxy server? > > > > Also, I noticed when looking at the Tool Dependency Definitions at > https://toolshed.g2.bx.psu.edu/ there are errors going back many versions > for this tool (see Test runs – Installation errors – Tool dependencies). > > > > Thank you for any help you can provide. > > > > Dori > > > > ** > > Dori Sajdak > > Senior Systems Administrator > > State University of NY at Buffalo > > Center for Computational Research > > 701 Ellicott St > > Buffalo, NY 14203 > > Phone: (
Re: [galaxy-dev] problems installing tool dependency
I’m still in a holding pattern on these Miller Lab tools. Has anyone responded to your requests from back in September? I emailed them in August as well and heard nothing. We have users at our university that want to use these tools on our Galaxy instance. If there is no way to get them to change it in the tool shed, is there a way I can install quicktree myself and then tell Galaxy the dependency is installed for the other Miller Lab tools? Thank you for any help you can provide. From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Wednesday, September 24, 2014 2:58 PM To: Will Holtz Cc: Sajdak, Doris; galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] problems installing tool dependency I've just looked at this as well, it appears that /pub4 is not exposed and does not allow you to change into it, but it does allow you to fetch if you request files under it via the full path. e.g.: nate@victory% ncftp ftp.sanger.ac.uk<http://ftp.sanger.ac.uk> ... Logged in to ftp.sanger.ac.uk<http://ftp.sanger.ac.uk>. ncftp / > ls ls-lR.gz.ok_to_rsyncREADME .request-for-update.lock .messagepub/ .request-for-update ncftp / > cd pub4 Could not chdir to pub4: server said: pub4: No such file or directory ncftp / > cd /pub4 Could not chdir to /pub4: server said: pub4: No such file or directory ncftp / > get /pub4/resources/software/quicktree/quicktree.tar.gz quicktree.tar.gz: 38.12 kB 124.19 kB/s ncftp / > I'll contact some folks in the Miller Lab to see if the tool can be updated to the path under /pub. On Wed, Sep 24, 2014 at 2:09 PM, Will Holtz mailto:who...@lygos.com>> wrote: I also was able to download quicktree.tar.gz by clicking on the URL in your message. However, when I manually ftp into ftp.sanger.ac.uk<http://ftp.sanger.ac.uk>, there is no /pub4 directory. I'm a bit confused about how those two statements are both true, but maybe it will help someone else figure this out. Removing the '4' does result in a valid path (ftp://ftp.sanger.ac.uk/pub/resources/software/quicktree/quicktree.tar.gz). -Will On Wed, Sep 24, 2014 at 10:57 AM, Sajdak, Doris mailto:dj...@buffalo.edu>> wrote: Hi all, I am trying to install the Genome Diversity tools from the Miller Lab that are in the Galaxy toolshed. I’ve been able to get all dependencies installed except Quicktree. Whenever I try to install it, I get the error: Error downloading from URL ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz: This is the tool_dependencies.xml file for installing quicktree: ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz make quicktree cp -R bin $INSTALL_DIR $INSTALL_DIR/bin I know this is not their file I’m downloading but the thing is, if I copy and paste the URL, I can download it with no problem. I’m not sure why it’s reporting that it can’t be found but the xml looks right to me. I’ve tried contacting the Miller Lab about this but haven’t heard from anyone so I’m hoping someone here can tell me how to move past this problem. Is there a way to install this tool manually and have the main Genome Diversity tools recognize it on the Galaxy server? Also, I noticed when looking at the Tool Dependency Definitions at https://toolshed.g2.bx.psu.edu/ there are errors going back many versions for this tool (see Test runs – Installation errors – Tool dependencies). Thank you for any help you can provide. Dori ** Dori Sajdak Senior Systems Administrator State University of NY at Buffalo Center for Computational Research 701 Ellicott St Buffalo, NY 14203 Phone: (716) 881-8934 Fax: (716) 849-6656 Web: http://ccr.buffalo.edu ** ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ 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 thi
