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phenoscape / Phenex

Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
http://phenex.phenoscape.org/
MIT License
10 stars 3 forks source link

starting up Phenex in Windows #36

Open balhoff opened 11 years ago

balhoff commented 11 years ago

First, each time I want to open Phenex, I have to open 2 files ("phenex-1.0.1-win" and "Phenex") and then I have to execute the MS-DOS command file called "Phenex"... I don't have any Phenex icon which would permit me to directly launch Phenex.

AnaisGrand commented 11 years ago

When I launch Phenex by double-clicking on Phenex.bat, I get an error about "javaw' which is missing...How can I fix this ? Thank you in advance for your answer

balhoff commented 11 years ago

@AnaisGrand can you tell me what version of Windows and Java you are using? I will see if I can reproduce the problem. We don't have too many Windows users so it might be a simple issue we haven't run into. Thank you!

AnaisGrand commented 11 years ago

I am using "Windows 7 professionel" 64 bits, and Java version 7 update 9 (32 bits). I've just downloaded the 64 bits version of java, and Phenex can be launched now ! Thank you for your answer !

balhoff commented 11 years ago

Wonderful, thanks for letting me know.

AnaisGrand commented 11 years ago

As soon as I try to write in Phenex, the interface freezes...

balhoff commented 11 years ago

@AnaisGrand do you see a tab that says "Graph View" in the interface? It is quite slow and you may be able to fix this problem by closing that tab. Please let me know if that helps. I have access to Windows XP in VMware, and I am seeing a problem with selecting ontology terms in the autocomplete menus. Do you also have this problem?

Thanks!

AnaisGrand commented 11 years ago

Dear Jim,

Thank you for your email. After closing the tab "Graph View", the interface still freezes... I can't select ontology terms...

Best wishes, Anaïs Grand

Jim Balhoff notifications@github.com a écrit :

@AnaisGrand do you see a tab that says "Graph View" in the
interface? It is quite slow and you may be able to fix this problem
by closing that tab. Please let me know if that helps. I have access
to Windows XP in VMware, and I am seeing a problem with selecting
ontology terms in the autocomplete menus. Do you also have this
problem?

Thanks!

Reply to this email directly or view it on GitHub: https://github.com/phenoscape/Phenex/issues/36#issuecomment-10723407

Anaïs Grand UMR7207 CR2P,CNRS, MNHN, UPMC 57 rue Cuvier 75005 Paris

balhoff commented 11 years ago

@AnaisGrand I haven't had any great ideas yet, but I wonder if you need to increase the memory used by Phenex. You can edit the Phenex.bat file in a text editor. You may want to try changing the value "-Xmx1024m" to "-Xmx2g". I will try to find a copy of 64-bit Windows to test with, but it may take me a while.

AnaisGrand commented 11 years ago

Dear Jim, Thank you for your help. I've tried with the value "-Xmx2g" and the interface still freezes.. Best wishes, Anais

Jim Balhoff notifications@github.com a écrit :

@AnaisGrand I haven't had any great ideas yet, but I wonder if you
need to increase the memory used by Phenex. You can edit the
Phenex.bat file in a text editor. You may want to try changing the
value "-Xmx1024m" to "-Xmx2g". I will try to find a copy of 64-bit
Windows to test with, but it may take me a while.

Reply to this email directly or view it on GitHub: https://github.com/phenoscape/Phenex/issues/36#issuecomment-11064321

Anaïs Grand UMR7207 CR2P,CNRS, MNHN, UPMC 57 rue Cuvier 75005 Paris

AnaisGrand commented 11 years ago

Dear Jim,

I have tried Phenex with MAC and it works. When I'm using "search panel", the suggested terms do not come from
the ontologies I have chosen (in the View -> Config menu). What do I need to do ?

Best regards, Anaïs

Jim Balhoff notifications@github.com a écrit :

@AnaisGrand I haven't had any great ideas yet, but I wonder if you
need to increase the memory used by Phenex. You can edit the
Phenex.bat file in a text editor. You may want to try changing the
value "-Xmx1024m" to "-Xmx2g". I will try to find a copy of 64-bit
Windows to test with, but it may take me a while.

Reply to this email directly or view it on GitHub: https://github.com/phenoscape/Phenex/issues/36#issuecomment-11064321

Anaïs Grand UMR7207 CR2P,CNRS, MNHN, UPMC 57 rue Cuvier 75005 Paris

balhoff commented 11 years ago

Hi Anaïs,

After entering in your ontology sources, make sure you press Apply and then relaunch Phenex, so that it will download the ontologies. I don't know if it is a problem for you, but unfortunately Phenex requires OBO-format ontologies for now.

Now you should have all your ontology terms loaded into Phenex. You can check by looking at the Complete Ontology Tree View. In order to have term suggestions in the entry fields, you need to configure search filters that Phenex uses to select the subset of terms it uses for each field. There is documentation here:

http://phenoscape.org/wiki/Phenex#Entry_field_filters

Basically you create a search and save it to a file with a special name that Phenex looks for.

I hope this helps.

AnaisGrand commented 11 years ago

Dear Jim,

Thank you for your answer. The problem was about downloading Plant Ontology. It seems that the
url available on the internet was not read by Phenex. I used another
url and now it works. I am going to use Phenex in the next days. May I get back to you if I
have other questions ? Thank you again for your help, Best regards, Anaïs

Jim Balhoff notifications@github.com a écrit :

Hi Anaïs,

After entering in your ontology sources, make sure you press Apply
and then relaunch Phenex, so that it will download the ontologies. I
don't know if it is a problem for you, but unfortunately Phenex
requires OBO-format ontologies for now.

Now you should have all your ontology terms loaded into Phenex. You
can check by looking at the Complete Ontology Tree View. In order to
have term suggestions in the entry fields, you need to configure
search filters that Phenex uses to select the subset of terms it
uses for each field. There is documentation here:

http://phenoscape.org/wiki/Phenex#Entry_field_filters

Basically you create a search and save it to a file with a special
name that Phenex looks for.

I hope this helps.

Reply to this email directly or view it on GitHub: https://github.com/phenoscape/Phenex/issues/36#issuecomment-12664672

Anaïs Grand UMR7207 CR2P,CNRS, MNHN, UPMC 57 rue Cuvier 75005 Paris

balhoff commented 11 years ago

Certainly - feel free to email me directly at balhoff@nescent.org.