Hi Ivan,

In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because

Unfortunately, rexpression is not supported at present- the source is readily available from bitbucket but the original author (me) stopped working on it. I'd be happy to hand the source on to others working in that space - it's in bitbucket. I think many people would agree that integrating gene expression and NGS variation data is a very interesting goal but I'm not aware of any tools to do that.

On Wed, Nov 9, 2011 at 7:10 AM, Ivan Merelli ivan.merelli@itb.cnr.it wrote:

Hi Galaxy Users,

I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu)

After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong?

In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening.

Cheers, Ivan

P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff..

Dear Eric, thank you for your answer. Your workaround works for the pheno file.

A related question is: the affybatch and the eset file formats require to upload two files (rispectively the pheno and the eset/affybatch).

Is it normal to have finally only the pheno one in the History?

I.

Hi Ivan,

I can provide an explanation about the first part at least. You are seeing that "##failed" message due to a bug in Galaxy core code that I've previously raised on this list. The path you see there is where the .pheno file should (and does) end up after the tool is done. However, the code that generates the "##failed" message is getting called before the .pheno file has been moved to that path from its temporary location. Hence, it can't be found there at that point in execution time.

While requiring a workaround is not ideal, a very simple one does exist. In the history item for your uploaded dataset, click on the pencil ("Edit attributes") and then click the button that says "Auto-detect".

Best, Eric

---

From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Ivan Merelli [ivan.merelli@itb.cnr.it] Sent: Wednesday, November 09, 2011 7:12 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] microarray& NGS

Hi Galaxy Users,

I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu)

After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong?

In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening.

Cheers, Ivan

P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff..

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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Hi Eric,

I'm using a local instance of galaxy, but I found an error also in the main public server (no debug, I suppose the same error).

When I try do download the pheno file I recieve this error: AttributeError: 'module' object has no attribute 'relpath'

Generally, I'm very interested in using galaxy for microarray analysis (for this reason I was checking the capability of rexpression) and if I can get involved someway in the development of this part (Eric, I did not understand if you are working on something new or if you are reviewing rexpression) I can help in testing/debug or giving suggestions (maybe also in developing, but I'm quite new of galaxy).

Best, I.

Hi Ivan,

That is correct, two files are uploaded. Both are stored in Galaxy's database (the filesystem part "database/files", not the relational part), and many subsequent operations on an affybatch or eset dataset will access the .affybatch or .eset file directly. Lines from the .pheno file are simply what those datatypes make the history item use for displaying info.

Having a single history item for both is normal for these datatypes. This is because the affybatch and eset datatypes are *composite* datatypes representing more than one file. This provides a mechanism for passing around a collection of related files as a single unit. The details and the implementation of composite datasets are a bit rough around the edges, but that's the concept. For instance, try downloading one of the affybatch or eset objects you've uploaded, by using the save button (ie the image of a tiny floppy disk in the history item). I'd be interested to know what happens for you (are you running a local instance or using the main public server?) and very interested to know if it works; it fails for me, but I've only had time so far to partially debug it.

Best, Eric

---

From: Ivan Merelli [ivan.merelli@itb.cnr.it] Sent: Friday, November 18, 2011 10:33 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] microarray& NGS

Dear Eric, thank you for your answer. Your workaround works for the pheno file.

A related question is: the affybatch and the eset file formats require to upload two files (rispectively the pheno and the eset/affybatch).

Is it normal to have finally only the pheno one in the History?

I.

...

Hi Ivan,

I can provide an explanation about the first part at least. You are seeing that "##failed" message due to a bug in Galaxy core code that I've previously raised on this list. The path you see there is where the .pheno file should (and does) end up after the tool is done. However, the code that generates the "##failed" message is getting called before the .pheno file has been moved to that path from its temporary location. Hence, it can't be found there at that point in execution time.

While requiring a workaround is not ideal, a very simple one does exist. In the history item for your uploaded dataset, click on the pencil ("Edit attributes") and then click the button that says "Auto-detect".

Best, Eric

---

From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Ivan Merelli [ivan.merelli@itb.cnr.it] Sent: Wednesday, November 09, 2011 7:12 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] microarray& NGS

Hi Galaxy Users,

I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu)

After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong?

In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening.

Cheers, Ivan

P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff..

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

Hi Eric,

sharing code for me is ok, so I can test it on my local instance of galaxy. Let me know if I can help in debugging or so on.

As concerning rexpression, I think is a good package, although some bugs (which I can summurize if useful, some of them were easy to solve) and features can be improved (such as for example the possibility to have exprSet in the history to work on differential expressed genes and eventually join this information with NGS data)

Let me know how I can help...

Best Ivan

Hi Ivan,

At the moment, my work is probably closer to "something new", but as I flesh it out and if I add more tools, it could start coming back toward rexpression development. I'd be glad to let you now when it is ready for testing, but can't promise exactly when that will be. Also, I'd only be able to give you code, not access to a test server, as our Galaxy instance is strictly internal. I do intend to try contributing anything that will be generally useful back to galaxy-central though.

Best, Eric

---

From: Ivan Merelli [ivan.merelli@itb.cnr.it] Sent: Saturday, November 19, 2011 10:40 AM To: Paniagua, Eric Cc: ross.lazarus@gmail.com; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] microarray& NGS

Hi Eric,

I'm using a local instance of galaxy, but I found an error also in the main public server (no debug, I suppose the same error).

When I try do download the pheno file I recieve this error: AttributeError: 'module' object has no attribute 'relpath'

Generally, I'm very interested in using galaxy for microarray analysis (for this reason I was checking the capability of rexpression) and if I can get involved someway in the development of this part (Eric, I did not understand if you are working on something new or if you are reviewing rexpression) I can help in testing/debug or giving suggestions (maybe also in developing, but I'm quite new of galaxy).

Best, I.

...

Hi Ivan,

That is correct, two files are uploaded. Both are stored in Galaxy's database (the filesystem part "database/files", not the relational part), and many subsequent operations on an affybatch or eset dataset will access the .affybatch or .eset file directly. Lines from the .pheno file are simply what those datatypes make the history item use for displaying info.

Having a single history item for both is normal for these datatypes. This is because the affybatch and eset datatypes are *composite* datatypes representing more than one file. This provides a mechanism for passing around a collection of related files as a single unit. The details and the implementation of composite datasets are a bit rough around the edges, but that's the concept. For instance, try downloading one of the affybatch or eset objects you've uploaded, by using the save button (ie the image of a tiny floppy disk in the history item). I'd be interested to know what happens for you (are you running a local instance or using the main public server?) and very interested to know if it works; it fails for me, but I've only had time so far to partially debug it.

Best, Eric

---

From: Ivan Merelli [ivan.merelli@itb.cnr.it] Sent: Friday, November 18, 2011 10:33 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] microarray& NGS

Dear Eric, thank you for your answer. Your workaround works for the pheno file.

A related question is: the affybatch and the eset file formats require to upload two files (rispectively the pheno and the eset/affybatch).

Is it normal to have finally only the pheno one in the History?

I.

...

Hi Ivan,

I can provide an explanation about the first part at least. You are seeing that "##failed" message due to a bug in Galaxy core code that I've previously raised on this list. The path you see there is where the .pheno file should (and does) end up after the tool is done. However, the code that generates the "##failed" message is getting called before the .pheno file has been moved to that path from its temporary location. Hence, it can't be found there at that point in execution time.

While requiring a workaround is not ideal, a very simple one does exist. In the history item for your uploaded dataset, click on the pencil ("Edit attributes") and then click the button that says "Auto-detect".

Best, Eric

---

From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Ivan Merelli [ivan.merelli@itb.cnr.it] Sent: Wednesday, November 09, 2011 7:12 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] microarray& NGS

Hi Galaxy Users,

I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu)

After processing the upload, the only message in the green output data box of the history is something like: ##failed to find /galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno Can you help me in understanding what's wrong?

In particular the data which I'm trying to upload are created with rexpression (incidentally, is it still supported or novel versions are attended?), because this package gives my some problems and I'm trying to upload manually some results (which seems ok on the disk) to see what is happening.

Cheers, Ivan

P.s. Maybe some other packages exists to deal with microarray data in Galaxy? e.g. retrieving data from GEO/ArrayExpress, normalizing them, show in a matrix differential expressed genes to join/confront them with novel NGS experiment... I know it's a lot of stuff..

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/