Image not available at Dockerhub

[greg-harhay]

Hi,

The link to docker hub doesn't work. I searched for your image at DockerHub and couldn't find it. I searched using icaoberg and found 3 images, none of which were associated with meme-suite. Thanks.

[icaoberg]

I deleted the image because I found some problems with one of the tools. I should be working this week on rebuilding the image.

Is there a particular tool you are interested in using?

[greg-harhay]

Meme, tomtom and fimo are the tools I use. I have a non-docker pipeline using these tools that I would like to convert into a docker-based one. Thanks.

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Friday, March 15, 2019 at 2:15 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Author author@noreply.github.com Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

I deleted the image because I found some problems with one of the tools. I should be working this week on rebuilding the image.

Is there a particular tool you are interested in using?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473410148, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AeBaq5zAnp7lrBAo0AHDCnsfsMCVYyCaks5vW_FIgaJpZM4b3IcW.

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[icaoberg]

I'm failing to compile meme properly. I will work on this and let you know.

On Fri, Mar 15, 2019 at 3:28 PM Gregory Harhay notifications@github.com wrote:

Meme, tomtom and fimo are the tools I use. I have a non-docker pipeline using these tools that I would like to convert into a docker-based one. Thanks.

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Friday, March 15, 2019 at 2:15 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Author < author@noreply.github.com> Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

I deleted the image because I found some problems with one of the tools. I should be working this week on rebuilding the image.

Is there a particular tool you are interested in using?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473410148>, or mute the thread< https://github.com/notifications/unsubscribe-auth/AeBaq5zAnp7lrBAo0AHDCnsfsMCVYyCaks5vW_FIgaJpZM4b3IcW>.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

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-- Ivan E. Cao-Berg Senior Research Programmer Computational Biology Department School of Computer Science Carnegie Mellon University

[greg-harhay]

Thank you !

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Friday, March 15, 2019 at 2:44 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Author author@noreply.github.com Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

I'm failing to compile meme properly. I will work on this and let you know.

On Fri, Mar 15, 2019 at 3:28 PM Gregory Harhay notifications@github.com wrote:

Meme, tomtom and fimo are the tools I use. I have a non-docker pipeline using these tools that I would like to convert into a docker-based one. Thanks.

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Friday, March 15, 2019 at 2:15 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Author < author@noreply.github.com> Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

I deleted the image because I found some problems with one of the tools. I should be working this week on rebuilding the image.

Is there a particular tool you are interested in using?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473410148>, or mute the thread< https://github.com/notifications/unsubscribe-auth/AeBaq5zAnp7lrBAo0AHDCnsfsMCVYyCaks5vW_FIgaJpZM4b3IcW>.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473413665, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZQODI3406LTIF_j9XI0WXvpa7LEMBlks5vW_REgaJpZM4b3IcW .

-- Ivan E. Cao-Berg Senior Research Programmer Computational Biology Department School of Computer Science Carnegie Mellon University

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[icaoberg]

Initial test results

============================================================================
Testsuite summary for meme 5.0.4
============================================================================
# TOTAL: 145
# PASS:  100
# SKIP:  21
# XFAIL: 0
# FAIL:  23
# XPASS: 0
# ERROR: 1
============================================================================
See tests/scripts/test-suite.log
============================================================================

[icaoberg]

Good news. It seems it passed most tests. I will update the formula and will push to Docker.

============================================================================
Testsuite summary for meme 5.0.4
============================================================================
# TOTAL: 145
# PASS:  131
# SKIP:  9
# XFAIL: 0
# FAIL:  4
# XPASS: 0
# ERROR: 1
============================================================================
See tests/scripts/test-suite.log
============================================================================

[greg-harhay]

Good news indeed. I’m ready to test on my end when image becomes available. Thanks again.

Greg

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Friday, March 15, 2019 at 5:33 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Author author@noreply.github.com Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

Good news. It seems it passed most tests. I will update the formula and will push to Docker.

============================================================================

Testsuite summary for meme 5.0.4

============================================================================

TOTAL: 145

PASS: 131

SKIP: 9

XFAIL: 0

FAIL: 4

XPASS: 0

ERROR: 1

============================================================================

See tests/scripts/test-suite.log

============================================================================

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473461840, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AeBaq0_hAArEc6lp8ccFzs9xg9emrO48ks5vXB-5gaJpZM4b3IcW.

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[icaoberg]

I'll do it after lunch. Sorry for the delay.

On Mon, Mar 18, 2019 at 12:35 PM Gregory Harhay notifications@github.com wrote:

Good news indeed. I’m ready to test on my end when image becomes available. Thanks again.

Greg

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Friday, March 15, 2019 at 5:33 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Author < author@noreply.github.com> Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

Good news. It seems it passed most tests. I will update the formula and will push to Docker.

============================================================================

Testsuite summary for meme 5.0.4

============================================================================

TOTAL: 145

PASS: 131

SKIP: 9

XFAIL: 0

FAIL: 4

XPASS: 0

ERROR: 1

============================================================================

See tests/scripts/test-suite.log

============================================================================

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473461840>, or mute the thread< https://github.com/notifications/unsubscribe-auth/AeBaq0_hAArEc6lp8ccFzs9xg9emrO48ks5vXB-5gaJpZM4b3IcW>.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/icaoberg/docker-meme-suite/issues/1#issuecomment-473994011, or mute the thread https://github.com/notifications/unsubscribe-auth/AAZQOJmAXZy2d0QaY7Lhmf4O08LvWLL0ks5vX8AzgaJpZM4b3IcW .

-- Ivan E. Cao-Berg Senior Research Programmer Computational Biology Department School of Computer Science Carnegie Mellon University

[icaoberg]

@greg-harhay I will document it, in the meantime

docker pull icaoberg/meme-suite:5.0.4

[greg-harhay]

Great. Pulling now. I’ll let you know how it goes tomorrow.

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Monday, March 18, 2019 at 3:36 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Mention mention@noreply.github.com Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

docker pull icaoberg/meme-suite:5.0.4

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[greg-harhay]

The MEME results appear to be reasonable. I did run into a minor annoyance though. For each motif calculation, the meme process outputs lots of output in the form of:

[57b8c212b5ac:00452] Read -1, expected 20992, errno = 1

[57b8c212b5ac:00457] Read -1, expected 20992, errno = 1

[57b8c212b5ac:00460] Read -1, expected 20992, errno = 1

[57b8c212b5ac:00460] Read -1, expected 20992, errno = 1

[57b8c212b5ac:00451] Read -1, expected 20992, errno = 1

[57b8c212b5ac:00452] Read -1, expected 10496, errno = 1

[57b8c212b5ac:00453] Read -1, expected 10496, errno = 1

[57b8c212b5ac:00457] Read -1, expected 10496, errno = 1

[57b8c212b5ac:00460] Read -1, expected 10496, errno = 1

Where 57b8c212b5ac is the container ID. Does this indicate that I haven’t setup my docker environment correctly? In any case this output doesn’t appear to have affected the meme results. From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Monday, March 18, 2019 at 3:36 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Mention mention@noreply.github.com Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

@greg-harhayhttps://github.com/greg-harhay I will document it, in the meantime

docker pull icaoberg/meme-suite:5.0.4

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[icaoberg]

@greg-harhay can you share the command you used so that I can replicate this warning?

[greg-harhay]

Hi,

Sure, I’ve attached a small input file. The command is:

meme CP004752.2_InterCDS_ROI_Between_400_And_100_from_CDS_Start.fasta -dna -evt 0.01 -nmotifs 100 -mod zoops -searchsize 0 -p 5 -brief 32000 -maxsize 10000000 -oc CP004752.2_InterCDS_ROI_Between_400_And_100_from_CDS_Start

Thanks for looking into this.

Best Regards,

Greg

From: icaoberg notifications@github.com Reply-To: icaoberg/docker-meme-suite reply@reply.github.com Date: Wednesday, April 10, 2019 at 9:54 PM To: icaoberg/docker-meme-suite docker-meme-suite@noreply.github.com Cc: Gregory Harhay Gregory.Harhay@ARS.USDA.GOV, Mention mention@noreply.github.com Subject: Re: [icaoberg/docker-meme-suite] Image not available at Dockerhub (#1)

@greg-harhayhttps://github.com/greg-harhay can you share the command you used so that I can replicate this warning?

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