Hi Martin, I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error:
Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation error:/bin/sh: -c: line 14: syntax error: unexpected end of file If you have any suggestions about this error, I'd be pleased to attempt to resolve it. Best, Scott On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi <scott.b.szakony...@nd.edu> wrote: > Hi Martin, > > Thanks very much for your reply, and also to Marius. > > After some investigation, it appears that there is a firewall issue on my > Galaxy server which is preventing the download of the file via FTP. I'm > looking into options for that now. > > Best, > > Scott > > On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech <mar...@bx.psu.edu> wrote: > >> Hello Scott, >> >> thanks to Marius van den Beek the first two issues should be fixed with >> this PR: https://github.com/galaxyproject/tools-devteam/pull/299 >> >> These changes were already propagated to the Main Tool Shed. >> Note for tool developers: for future endeavours please use packages from >> the IUC repository ( >> https://github.com/galaxyproject/tools-iuc/tree/master/packages) >> >> As of the timeout for the readline package it seems the problem was on >> the ftp.gnu side and it is now resolved. >> In the future Galaxy plans to use a smart caching proxy to handle&mirror >> all source codes required by the Tool Shed installations. This effort is >> lead by Eric Rasche and you can see it here >> https://github.com/galaxyproject/cargo-port >> >> Thank you for the report (and for using Galaxy :)). >> >> Martin >> >> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < >> scott.b.szakony...@nd.edu> wrote: >> >>> Hi all, >>> >>> I'm installing the latest revision of Picard tools (efc56ee1ade4). >>> Picard installs successfully, and the tools are appearing in the >>> appropriate menu, but several packages that install with Picard are >>> reporting dependency issues, and I'm concerned that not all the tools will >>> work appropriately. The tools reporting issues are: >>> >>> - package_cairo_1_12_14 (last lines of long warning/error sequence) >>> - >>> >>> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: >>> file not recognized: Is a directory >>> collect2: ld returned 1 exit status >>> make[3]: *** [libcairo.la] Error 1 >>> make[2]: *** [all] Error 2 >>> make[1]: *** [all-recursive] Error 1 >>> make: *** [all] Error 2 >>> - package_pixman_0_32_4 >>> - >>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In >>> function `_start': >>> (.text+0x20): undefined reference to `main' >>> collect2: ld returned 1 exit status >>> make[2]: *** [clip-test] Error 1 >>> make[1]: *** [all-recursive] Error 1 >>> make: *** [all] Error 2 >>> - package_readline_6_2 >>> - Error downloading from URL >>> ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: >>> <urlopen error ftp error: [Errno 110] Connection timed out> >>> >>> Is anyone else having issues with these packages? Any suggestions for >>> resolving these problems? >>> >>> Thanks! >>> >>> -- >>> Scott B. Szakonyi >>> Research Programmer >>> >>> *Center for Research Computing* >>> 107 Information Technology Center >>> Notre Dame, IN 46556 >>> http://crc.nd.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: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >> >> > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu
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