Guys, I can express how thankful I am for your help!!!
Personally, I would comment out the following line in the tbl2asn code:
8869http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8869 if (MoreThanYearOldhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=MoreThanYearOld ()) { 8870http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8870 too_old = TRUEhttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=TRUE; 8871http://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c#L8871 Messagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/ident?i=Message (MSG_POSThttp://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."); 8872http://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.commailto:p.j.a.cock@googlemail.com> wrote: On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <edgar.fernandez@umontreal.camailto: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