Add cmd-line option to open file

Question

Add cmd-line option to open file

pgdurand opened this issue 8 years ago · comments

Add a cmd-line option at least to open file when starting BV from the cmd-line

Brian Fristensky · Answer 1 · Tue Jun 23 2020 02:46:05 GMT+0800 (China Standard Time)

What is the syntax for opening blastviewer with a file from the Linux command line? I have tried numerous things, including fully qualified paths, but blastviewer always pops up empty.
eg.
java -jar blastviewer-5.3.0.jar mousecat.blastn.xml

I know the file is good, because I can read it manually into blastviewer using the Open button.

I am particularly interested in getting this to work because blastviewer would be a nice addition to my BIRCH bioinformatics system. BIRCH runs BLAST searches from a GUI, and pops up output in a web browser and a spreadsheet-style program. A tutorial illustrating how this works can be found at
[http://home.cc.umanitoba.ca/~psgendb/birchhomedir/BIRCHDEV/public_html/tutorials/bioLegato/blastdb/blastdb.html]
Getting output to come up in blastviewer would expand the user's ability to work with the output.

Patrick Durand · Answer 2 · Tue Jun 23 2020 18:08:37 GMT+0800 (China Standard Time)

well I didn't add this feature until now... however, 2 years ago I started the dev of the Java Web Start release of BlastViewer that is capable of doing what you'd like to do (look at the 'jws' branch of BlastViewer project on Github)... but, Oracle stopped the use of JWS, so I do not know what direction to follow...

Brian Fristensky · Answer 3 · Tue Jun 30 2020 08:00:35 GMT+0800 (China Standard Time)

My own interest would be in blastviewer as a standalone desktop application, rather than using JWS.
The idea behind BIRCH is to have a seamless flow of data from one step to the next. BIRCH has its own spreadsheet-style program for displaying and retrieving BLAST hits, but blastviewer is such a full-featured and intuitive program that I'd like to be able to have output also pop up in blastviewer.

My guess is that adding a command line option for the input file would be easy. Let me know if you are willing to add this feature.
Thanks!

Patrick Durand · Answer 4 · Fri Jul 03 2020 21:13:21 GMT+0800 (China Standard Time)

ok, I understand your query... I think I should have some time during July to add that command-line option to the software... stay tuned !

Brian Fristensky · Answer 5 · Sat Jul 04 2020 01:46:21 GMT+0800 (China Standard Time)

Great. If it's any incentive, I tried a lot of blast output viewers, and was most impressed with blastviewer. I'm looking forward to seeing the revised version.

Patrick Durand · Answer 6 · Fri Jul 24 2020 17:12:13 GMT+0800 (China Standard Time)

Hi.

Work done, please read:
https://github.com/pgdurand/BlastViewer/wiki#use-command-line-arguments

Checkout latest release of BlastViewer implementing command-line arguments:
https://github.com/pgdurand/BlastViewer/releases/tag/v5.4.0

Let me know whether implemented features fit your needs.

Brian Fristensky · Answer 7 · Fri Jul 24 2020 22:16:38 GMT+0800 (China Standard Time)

Many thanks. I'll give it a try tomorrow. ==================================================== Brian Fristensky Department of Plant Science University of Manitoba Winnipeg, MB R3T 2N2 CANADA Phone: 204-474-6085 FAX: 204-474-7528 frist@cc.umanitoba.ca<mailto:frist@cc.umanitoba.ca> http://home.cc.umanitoba.ca/~frist/<http://home.cc.umanitoba.ca/~frist> =========================================================== I can't say that running is my favorite thing to do in space: after you get used to floating everywhere, it feels odd and a little unfair to have to move your legs to go nowhere.... Astronauts who are serious runners seem to mind less; in 2007, Suni Wiliams ran the Boston Marathon in space, which took her only 4 hours and 24 minutes. -- Chirs Hadfield, AN ASTRONAUT'S GUIDE TO LIFE ON EARTH. ===========================================================

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________________________________ From: Patrick Durand <notifications@github.com> Sent: July 24, 2020 04:12 To: pgdurand/BlastViewer Cc: Brian Fristensky; Comment Subject: Re: [pgdurand/BlastViewer] Add cmd-line option to open file (#3) Caution: This message was sent from outside the University of Manitoba. Hi. Work done, please read: https://github.com/pgdurand/BlastViewer/wiki#use-command-line-arguments Checkout latest release of BlastViewer implementing command-line arguments: https://github.com/pgdurand/BlastViewer/releases/tag/v5.4.0 Let me know whether implemented features fit your needs. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#3 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHBFH6XIH6LWQLSLP6LYZO3R5FGABANCNFSM4C2KWFNQ>.