Guys, I can express how thankful I am for your help!!!
Personally, I would comment out the following line in the tbl2asn code:
|
8871
Message
(MSG_POST,
"This copy of tbl2asn is more than a year old. Please download the current version."); 8872
} |
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> 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