4:16 p.m.
Hi,
I'm currently using ergatis as workflow manager, and I'm looking at the
differences
between ergatis and galaxy. In order maybe to migrate to galaxy.
One really important feature to me is the ability of ergatis to iterate
against file liste.
I haven't seen anything like this in galaxy, am I mistaking ?
Other point there is a way to make galaxy using local files instead of
importing all
files on the server ?
And finaly I was wondering if there is a way to configure galaxy, so the
outputs are
stored to the ldap-user home directory ?
thanks for your reply,
Jerome
5:52 p.m.
On 2/5/10 5:16 PM, "Mariette" <jmariett(a)toulouse.inra.fr> wrote:
Hi,
I'm currently using ergatis as workflow manager, and I'm looking at the
differences
between ergatis and galaxy. In order maybe to migrate to galaxy.
One really important feature to me is the ability of ergatis to iterate
against file liste.
I haven't seen anything like this in galaxy, am I mistaking ?
Other point there is a way to make galaxy using local files instead of
importing all files on the server ?
And finaly I was wondering if there is a way to configure galaxy, so the
outputs are stored to the ldap-user home directory ?
Jerome
Well, I am tempting to say: 'everything' is possible with galaxy.
Galaxy is so brilliant, because, you can easily modify the existing tools
and you can add pretty much any tool you want (as long as it can be called
from the command line). In our local Galaxy installation, we have added
several tools which rely on files outside of the galaxy directory tree.
Storing results in user home directories might be a little bit tricky, but I
don't see major problems, as long as the server on which galaxy runs has
access to the home directories, each home directory has a designated area
with write permission for the 'user' galaxy and the individual users are
logged in when they use galaxy....you will need to discuss this with your
sysadmin.
Once you have been using galaxy, you will probably realize, that you don't
want to store results in home directories...especially if you work with
large files (eg NGS). Take advantage of Galaxy, where every user has his/her
own history (i.e. the datasets) on a central server.
Enough "blabla" from my site - just download and install Galaxy. And you
will soon realize its potential.
Hans
thanks for your reply,
Jerome
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6:11 p.m.
Hi Hans and Jerome,
On Feb 5, 2010, at 6:52 PM, Hotz, Hans-Rudolf wrote:
On 2/5/10 5:16 PM, "Mariette"
<jmariett(a)toulouse.inra.fr> wrote:
> Hi,
>
> I'm currently using ergatis as workflow manager, and I'm looking at the
> differences
> between ergatis and galaxy. In order maybe to migrate to galaxy.
> One really important feature to me is the ability of ergatis to iterate
> against file liste.
> I haven't seen anything like this in galaxy, am I mistaking ?
> Other point there is a way to make galaxy using local files instead of
> importing all files on the server ?
> And finaly I was wondering if there is a way to configure galaxy, so the
> outputs are stored to the ldap-user home directory ?
Jerome
Well, I am tempting to say: 'everything' is possible with galaxy.
Although I do agree that Galaxy is a great tool :), one of the things Jerome asked is
actually not possible: iterating over a list of files is currently a no go unless you want
to click yourself into a sick leave due to RSI. This is something I would love to see as
in some of our experiments we generate big collections of files. For example we use LC
separation before MS usually generating something like 12 * 12 = 144. Manually uploading
144 files for processing in Galaxy is not fun. As a workaround we can sometimes merge the
data from the fractions before uploading, but in that case you easily loose the link
between the identified peptides and which fraction it was derived from, so this is
suboptimal...
So, more complex workflows with splitting, merging, looping, etc. are not (yet) possible
with Galaxy as far as I know, but because Galaxy does not do this complex stuff, you
don't need a manual to get started: KIS :).
Cheers,
Pi
Galaxy is so brilliant, because, you can easily modify the existing
tools
and you can add pretty much any tool you want (as long as it can be called
from the command line). In our local Galaxy installation, we have added
several tools which rely on files outside of the galaxy directory tree.
Storing results in user home directories might be a little bit tricky, but I
don't see major problems, as long as the server on which galaxy runs has
access to the home directories, each home directory has a designated area
with write permission for the 'user' galaxy and the individual users are
logged in when they use galaxy....you will need to discuss this with your
sysadmin.
Once you have been using galaxy, you will probably realize, that you don't
want to store results in home directories...especially if you work with
large files (eg NGS). Take advantage of Galaxy, where every user has his/her
own history (i.e. the datasets) on a central server.
Enough "blabla" from my site - just download and install Galaxy. And you
will soon realize its potential.
Hans
> thanks for your reply,
> Jerome
> _______________________________________________
> galaxy-user mailing list
> galaxy-user(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user
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2 comments
3 participants
participants (3)
-
Hotz, Hans-Rudolf -
Mariette -
Pieter Neerincx