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Update t-coffee to 13.45.0.4846264 #25932

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merged 3 commits into from Dec 23, 2020
Merged

Update t-coffee to 13.45.0.4846264 #25932

merged 3 commits into from Dec 23, 2020

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@nsoranzo
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@nsoranzo nsoranzo commented Dec 22, 2020 •
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This is the compiled T-Coffee package.

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

  • If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
  • New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
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@nsoranzo nsoranzo force-pushed the t_coffee_13.45.0.4846264 branch 2 times, most recently from 725e8ff to 0dc600f Dec 22, 2020
@nsoranzo nsoranzo changed the title Update t_coffee to 13.45.0.4846264 Update t-coffee to 13.45.0.4846264 Dec 22, 2020
@nsoranzo nsoranzo force-pushed the t_coffee_13.45.0.4846264 branch 6 times, most recently from f12c723 to 7eafa3b Dec 23, 2020
nsoranzo added 3 commits Dec 23, 2020
@nsoranzo
Update t-coffee to 13.45.0.4846264
8cf87e2
@nsoranzo
Skip osx
c5e5e25 
Just running `t_coffee` fails with:
```
04:33:21 BIOCONDA INFO (OUT) -max_n_proc    	D	[0] 	1
04:33:21 BIOCONDA INFO (OUT)
04:33:21 BIOCONDA INFO (OUT)
04:33:21 BIOCONDA INFO (OUT) *************************************************************************************************
04:33:21 BIOCONDA INFO (OUT) *                        FULL TRACE BACK PID: 2901
04:33:21 BIOCONDA INFO (OUT) 2901 -- ERROR: COREDUMP: T-COFFEE Version_13.45.32.7d81f5b (2020-12-18 11:45:26 - Revision 7d7e789 - Build 647)
04:33:21 BIOCONDA INFO (OUT) *************************************************************************************************
04:33:21 BIOCONDA INFO (OUT)
04:33:21 BIOCONDA INFO (OUT) 	******************************************************************
04:33:21 BIOCONDA INFO (OUT) 	* Abnormal Termination
04:33:21 BIOCONDA INFO (OUT) 	* Job NOT Completed:[T-COFFEE, Version_13.45.32.7d81f5b]
04:33:21 BIOCONDA INFO (OUT) 	* Please CHECK:
04:33:21 BIOCONDA INFO (OUT) 	* 	-1 The format of your Input Files
04:33:21 BIOCONDA INFO (OUT) 	* 	-2 The parameters
04:33:21 BIOCONDA INFO (OUT) 	* 	-3 The use of special characters in sequence names:
04:33:21 BIOCONDA INFO (OUT) 	* 		 (@, |, %...)
04:33:21 BIOCONDA INFO (OUT) 	* 	-4 The Online Doc (http://www.tcoffee.org)
04:33:21 BIOCONDA INFO (OUT) 	* 	-5 re-run your CL (see below) with the -debug option. This will produce a debug file you can send us.
04:33:21 BIOCONDA INFO (OUT) 	*
04:33:21 BIOCONDA INFO (OUT) 	*	    NO
04:33:21 BIOCONDA INFO (OUT) 	* to:
04:33:21 BIOCONDA INFO (OUT) 	* 		cedric.notredame@gmail.com
04:33:21 BIOCONDA INFO (OUT) 	* If you run T-Coffee over the WEB:
04:33:21 BIOCONDA INFO (OUT) 	* 	Windows Cut and Paste is sometimes erratic and
04:33:21 BIOCONDA INFO (OUT) 	* 	it can loose carriage returns. If you suspect this,
04:33:21 BIOCONDA INFO (OUT) 	* 	try to cut and paste through an intermediate application
04:33:21 BIOCONDA INFO (OUT) 	* 	(word pad) and inspect the results
04:33:21 BIOCONDA INFO (OUT)
04:33:21 BIOCONDA INFO (OUT)
04:33:21 BIOCONDA INFO (OUT) 	* CONFIDENTIALITY:
04:33:21 BIOCONDA INFO (OUT) 	* 	The File NO may contain your personal DATA
04:33:21 BIOCONDA INFO (OUT) 	* 	Remove ALL confidential DATA from this file BEFORE sending it
04:33:21 BIOCONDA INFO (OUT) 	******************************************************************
04:33:21 BIOCONDA INFO (OUT) # Command Line: t_coffee  [PROGRAM:T-COFFEE]
04:33:21 BIOCONDA INFO (OUT)
04:33:21 BIOCONDA INFO (OUT) # TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 2901 ppid 2895
04:33:21 BIOCONDA INFO (OUT) #CL: t_coffee
```
@nsoranzo
Add [de]activate scripts
7eafa3b 
to workaround cbcrg/tcoffee#27
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@nsoranzo nsoranzo commented Dec 23, 2020

@BiocondaBot please fetch artifacts

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@bioconda bioconda deleted a comment from BiocondaBot Dec 23, 2020
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@BiocondaBot BiocondaBot commented Dec 23, 2020

Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
linux-64 t-coffee-13.45.0.4846264-he1b5a44_0.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages on linux-64:
conda install -c https://135169-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
t-coffee 13.45.0.4846264--he1b5a44_0
showcurl "https://135169-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/t-coffee%3A13.45.0.4846264--he1b5a44_0.tar.gz" | gzip -dc | docker load

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@nsoranzo
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@nsoranzo nsoranzo commented Dec 23, 2020

@BiocondaBot please merge

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@nsoranzo
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@nsoranzo nsoranzo commented Dec 23, 2020

Thanks @dpryan79 !

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@BiocondaBot BiocondaBot commented Dec 23, 2020

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

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@BiocondaBot BiocondaBot merged commit 47c10bb into bioconda:master Dec 23, 2020
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@nsoranzo nsoranzo deleted the t_coffee_13.45.0.4846264 branch Dec 23, 2020
@nsoranzo nsoranzo mentioned this pull request Dec 24, 2020
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