If I understand it correctly; You have to check the sanitize option for your tool. The pipe (among others) is usually by default sanitised into X. Alex

Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens KOH Jia Yu Jayce Verzonden: donderdag 4 augustus 2011 8:52 Aan: 'galaxy-dev@lists.bx.psu.edu' Onderwerp: [galaxy-dev] filter

Filter and Sort -> Filter

I filtered with the following criterion

c16=='|'

but in the final output it shows as

Filtering with c16=='X'

and obviously the output contains nothing.

is this a bug or some feature?

After I used <sanitizer sanitize="False"/> the problem was solved.

Is the error intentional and has consequences that we might have missed? Or is it a bug?

holidays.....so don't have my files here. It is applicable to a local galaxy instance as you probably figured out. You cannot do anything on the public galaxy instance. The documentation is here; option 21 sanitize. What you basically do is to exclude specific characters like the pipe from being sanitised. The grep option as mentioned at 21 is a good example that should explain it. http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Good luck.

________________________________ Van: KOH Jia Yu Jayce [kohj3@gis.a-star.edu.sg] Verzonden: maandag 15 augustus 2011 6:02 Aan: Bossers, Alex CC: 'galaxy-dev@lists.bx.psu.edu' Onderwerp: RE: filter

Hi thanks, but what sanitizer option should I set it to?

-----Original Message----- From: Bossers, Alex [mailto:Alex.Bossers@wur.nl] Sent: Thursday, August 04, 2011 3:11 PM To: KOH Jia Yu Jayce Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: RE: filter

If I understand it correctly; You have to check the sanitize option for your tool. The pipe (among others) is usually by default sanitised into X. Alex

Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens KOH Jia Yu Jayce Verzonden: donderdag 4 augustus 2011 8:52 Aan: 'galaxy-dev@lists.bx.psu.edu' Onderwerp: [galaxy-dev] filter

Filter and Sort -> Filter

I filtered with the following criterion

c16=='|'

but in the final output it shows as

Filtering with c16=='X'

and obviously the output contains nothing.

is this a bug or some feature?

After I used <sanitizer sanitize="False"/> the problem was solved.

Is the error intentional and has consequences that we might have missed? Or is it a bug?

Hi Jayce,

Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon.

Thanks,

K

On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce kohj3@gis.a-star.edu.sgwrote:

In running macs in galaxy, the following error was found

ERROR:root:mfold format error! Your input is '32'. It should be like '10,30'

A format for mfold like 10,30 is expected… but the default value configured in xml remains as 32. will there be an updated version of this xml in future?

Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30?

Thanks alot

---

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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You can use the MACS wrappers here (for 1.4): https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakc...

Until we officially add it to our distribution.

Thanks,

K

On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce kohj3@gis.a-star.edu.sgwrote:

Yes. Thank you for your help J

-----Original Message----- *From:* Kanwei Li [mailto:kanwei@gmail.com] *Sent:* Wednesday, August 24, 2011 11:28 PM *To:* KOH Jia Yu Jayce *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] macs in galaxy

Hi Jayce,

Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon.

Thanks,

K

On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce kohj3@gis.a-star.edu.sg wrote:

In running macs in galaxy, the following error was found

ERROR:root:mfold format error! Your input is '32'. It should be like '10,30'

A format for mfold like 10,30 is expected… but the default value configured in xml remains as 32. will there be an updated version of this xml in future?

Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30?

Thanks alot

---

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/

Hello,

Perhaps you have found this in the source already, but if not, a version of the Tophat tool for SOLiD is available. It is on the test server only, should be used with caution, and is completely unsupported.

In the Galaxy source at bitbucket, please see: tophat_color_wrapper.xml at https://bitbucket.org/galaxy/galaxy-central/src/b751663f3f64/tools/ngs_rna

On the Galaxy test server under "NGS: RNA Analysis -> Tophat for SOLiD" http://test.g2.bx.psu.edu/

Hopefully this helps!

Best,

Jen Galaxy team

On 9/6/11 12:47 AM, KOH Jia Yu Jayce wrote:

Hi,

I am looking for tophat xml that supports SOLID colorspace. Is it anywhere available?

Thanks a lot.

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I don't believe so, it looks like they generate a long config script (as you can see in the xml file) and executes that.

K

On Thu, Sep 8, 2011 at 1:51 PM, Chorny, Ilya ichorny@illumina.com wrote:

Is there a python script associated with the macs.xml file?****

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*From:* galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edu] *On Behalf Of *Kanwei Li *Sent:* Wednesday, August 24, 2011 5:41 PM

*To:* KOH Jia Yu Jayce *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] macs in galaxy****

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You can use the MACS wrappers here (for 1.4): https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakc...

---

---

Until we officially add it to our distribution. ****

---

Thanks,****

---

K****

On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce kohj3@gis.a-star.edu.sg wrote:****

Yes. Thank you for your help J****

---

-----Original Message----- *From:* Kanwei Li [mailto:kanwei@gmail.com] *Sent:* Wednesday, August 24, 2011 11:28 PM *To:* KOH Jia Yu Jayce *Cc:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] macs in galaxy****

---

Hi Jayce,****

---

Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon.****

---

Thanks,****

---

K****

On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce kohj3@gis.a-star.edu.sg wrote:****

In running macs in galaxy, the following error was found****

---

ERROR:root:mfold format error! Your input is '32'. It should be like '10,30'****

---

A format for mfold like 10,30 is expected… but the default value configured in xml remains as 32. will there be an updated version of this xml in future?****

---

Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30?****

---

Thanks alot****

---

---

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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/****

---

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On Sep 29, 2011, at 11:02 PM, KOH Jia Yu Jayce wrote:

Hi

I’d like to enquire about the bug report. Apparently when someone sends a bug report, everyone in the mailing list and the sender himself are supposed to receive the bug report (as can be seen in the to field in the email sent out). However in our case the sender never receives the bug report even though his email address is in the to field.

How do we resolve the issue such that everyone including the sender receives the bug report?

In the universe config file, error_email_to = galaxy_dev@mailman.gis.a-star.edu.sg was set.

Hi,

I've just submitted a fix for this to the in-development source tree, and it'll be part of our next stable release. Thanks for reporting this issue and for using Galaxy.

--nate

Thanks so much!

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Hi,

I have a question. While trying to view bed tracks on UCSC by clicking on display at UCSC_main, the data on URL used to upload on UCSC:

http://galaxy/root/display_as?id=8155&display_app=ucsc&authz_method=...

was of bed 6 format. I am intrigued since the original data at galaxy history page with which we use to view at UCSC is of bed 12 format.

Can anyone explain why this happened? Thank you so much!