load genom by selecting file ?

[dridk]

as @natir suggest, it's a bad idea, to have one folder for genomes.
Create from the Menu : Genom > open genom, Annotation > open annotation

[dridk]

At the end, I m not sure it's a good idea.
We are going to preprocess file and create associated index file.
Also, from the user side, it's easier to have one place to store everything.
For instance, steam application, download and manage everything from the same place.
Let's discuss about it

[dridk]

In the other hand, I do not want to import my annotation file ... !

[dridk]

Let's do like IGV !
Genome file are imported into a common folder.
But annotation a read directly from their location.

[natir]

I don't understand why bigbroswer required a special directory for file.
File generate by bigbroswer is save is same directory of original file.

I didn't see the problem and create a bigbroswer directory in home directory of the user is disgusting.

[dridk]

I partially agree.
When I created the folder path, I was thinking of a download manager which
download genom and annotation from server.
When application start, It loads available genom name and display them into
the genom combobox. To do that, I have to scan a defined folder.

I think you are right for annotation local file, which can reside
anywhere.
But what about downloaded file from bigbrother? Where must they go?

To summarise, they are 2 kind of data.

• genome package from local or network
• annotation from local or network

When you click on AddData, a dialog box should appear which allows user to
select data from local or from server

Le 1 avr. 2016 21:42, "Pierre Marijon" [email protected] a écrit :

I don't understand why bigbroswer required a special directory for file.
File generate by bigbroswer is save is same directory of original file.

I didn't see the problem and create a bigbroswer directory in home
directory of the user is disgusting.

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[natir]

If the question is where store the download file ? The answer is in same for all application in the download directory (but user can set this parameter).

We can use this to find it http://doc.qt.io/qt-5/qstandardpaths.html

[dridk]

What about genomes files? And how to make application understand that some
annotation file works only with a genom file .

2016-04-02 9:28 GMT+02:00 Pierre Marijon [email protected]:

If the question is where store the download file ? The answer is in same
for all application in the download directory (but user can set this
parameter).

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Sacha schutz
Interne en Biologie moléculaire
Bioinformaticien
+33651571606
dridk.me
Fork me on github https://github.com/

[natir]

It's the user responsibility to be sure the annotation file match with sequence file.

[dridk]

And about download folder,
what about having annotationDownloadFolder , with subfolder ordered by
categories.

annotation / hg19 / gcPercent.bed

2016-04-02 11:20 GMT+02:00 Pierre Marijon [email protected]:

It's the user responsibility to be sure the annotation file match with
sequence file.

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Sacha schutz
Interne en Biologie moléculaire
Bioinformaticien
+33651571606
dridk.me
Fork me on github https://github.com/

[natir]

For your example, User add track and after in the track setting select file we want

I didn't understand why you want a strict subfolder organization let the user to be free. I hate application we force me to use special file organization. Application work for me, I didn't work for application.

[dridk]

I understand your point.
But In most of the case, user will download items from download manager. I
m talking about this point.

2016-04-02 11:37 GMT+02:00 Pierre Marijon [email protected]:

For your example, User add track and after in the track setting select
file we want

I didn't understand why you want a strict subfolder organization let the
user to be free. I hate application we force me to use special file
organization. Application work for me, I didn't work for application.

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#55 (comment)

Sacha schutz
Interne en Biologie moléculaire
Bioinformaticien
+33651571606
dridk.me
Fork me on github https://github.com/

[natir]

Yes and file is download in system download dir, and if user want move/remove/modified file BB is ok.

In your approach BB is good for one use case :

• User download file with BB
• User see file with BB

In my approach BB is good for all more use case :

• User download/build/create file with any software
• User see any file with BB

[dridk]

So let's do annotation as you said .
But genom should be application file.

2016-04-02 12:05 GMT+02:00 Pierre Marijon [email protected]:

Yes and file is download in system download dir, and if user want
move/remove/modified file BB is ok.

In your approach BB is good for one use case :

• User download file with BB
• User see file with BB

In my approach BB is good for all more use case :

• User download/build/create file with any software
• Use see any file with BB

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#55 (comment)

Sacha schutz
Interne en Biologie moléculaire
Bioinformaticien
+33651571606
dridk.me
Fork me on github https://github.com/