Hi Fernandez, 2015-09-29 10:02 GMT-05:00 Fernandez Edgar <edgar.fernandez@umontreal.ca>:
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 would replace the files. We (The IUC, specifically Björn and myself) have talked about solutions to this problem but haven't finished building them yet.
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?
You can fetch a precompiled version of tbl2asn here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/ I recommend replacing all of those (or just the first and last, assuming you're on linux) as (eventually) none of them will work. Hopefully in the future we'll be able to fix this.
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> wrote:
On Tue, Sep 29, 2015 at 1:12 PM, Fernandez Edgar <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
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Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu