Guys, I can express how thankful I am for your help!!! Personally, I would comment out the following line in the tbl2asn code: 8869<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8869> if (MoreThanYearOld<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MoreThanYearOld> ()) { 8870<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8870> too_old = TRUE<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=TRUE>; 8871<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8871> Message<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=Message> (MSG_POST<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MSG_POST>, "This copy of tbl2asn is more than a year old. Please download the current version."); 8872<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8872> } In the meantime, would you suggest I change the files located inside my galaxy installation? Or should I wait for Philip’s release? I ask because I found the following binary files: -rwxr-x--- 1 galaxy users 7349340 Sep 15 08:52 ./tool-data/toolshed.dependency.dir/tbl2asn/23.7/takadonet/package_tbl2asn_23_7/2271d52a8531/bin/tbl2asn -rwxrwxr-x 1 galaxy users 12675348 Jul 28 2014 ./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/darwin/tbl2asn -rwxrwxr-x 1 galaxy users 6872896 Jul 28 2014 ./tool-data/toolshed.dependency.dir/prokka/1.10/crs4/prokka/3ad7ef0ba385/binaries/linux/tbl2asn Oddly, they’re all different. What exactly can I do with this and how can I compile the tblasn.c file? Cordialement / Regards, Edgar Fernandez De : Philip Mabon [mailto:philipmabon@gmail.com] Envoyé : September-29-15 10:27 AM À : Peter Cock; Fernandez Edgar; Nicola Soranzo (TGAC) Cc : Björn Grüning; galaxy-dev@bx.psu.edu Objet : Re: [galaxy-dev] not sure what I can do about this... I will make a new package for tbl2asn. Our lab is not too happy that tbl2asn expires and causes lots of issues for us. On Tue, Sep 29, 2015 at 9:24 AM Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote: On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <edgar.fernandez@umontreal.ca<mailto:edgar.fernandez@umontreal.ca>> wrote:
Hello Björn,
Thank you for answering! When I installed Prokka from the Galaxy ToolShed, all the dependencies were installed too. tbl2asn is one of those dependencies... How would I replace it?
Cordialement / Regards, Edgar Fernandez
The way the NCBI deliberately make tbl2asn expire is very annoying for packaging and breaks strict reproducibility :( I think Bjoern was suggesting manually updating the copy of tbl2asn which the Tool Shed had downloaded (as a quick short term solution). You'd need to find this file within the Tool Shed dependencies folder... Philip - can you update package_tbl2asn_23_7 or add a new package if the version number has changed? Or would you like the IUC group to look after this in future? https://toolshed.g2.bx.psu.edu/view/takadonet/package_tbl2asn_23_7/ Nicola - once that's done, can you update the prokka dependency list - or would that fall to your old colleagues at CRS4? https://toolshed.g2.bx.psu.edu/view/crs4/prokka/ Peter