g***@soe.ucsc.edu
2014-09-30 17:17:20 UTC
=============================================================================
Today's topic summary
=============================================================================
Group: ***@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics
- plotting read counts on the plus and minus strand [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
- problems to access bigwikg on our server [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
- gene coordinates in refGene.txt [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4f7908b05cdc4797
- Need help with running BLAT on CentOS [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
- Genome Browser question [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
- A bug in table browser? [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
- Error message for the bisulfite-seq subtrack for the ovary sample from Roadmap Epigenomics Data Complete Collection at Wash U VizHub [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cafb1bf0a0c5789e
- Transcription factors data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
=============================================================================
Topic: plotting read counts on the plus and minus strand
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
=============================================================================
---------- 1 of 1 ----------
From: "Yeroslaviz, Assa" <***@biochem.mpg.de>
Date: Sep 30 03:58PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1cd3dc427d323106
Hi,
I was wondering how I can plot my read counts in a strand specific way on the UCSC browser.
I would like to have the count for the gene on the plus strand to go up, while the reads mapped to the minus strand will be shown downwards.
Something like this:
[cid:B633FE69-92DD-4339-B8F0-15026C5A2445]
Is it possible to separate the two strands according to a specific parameter?
Thanks
Assa
=============================================================================
Topic: problems to access bigwikg on our server
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
=============================================================================
---------- 1 of 1 ----------
From: "Dr. Eyal Eran" <***@sheba.health.gov.il>
Date: Sep 30 03:06PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a2cc165e6036fb8e
Dear UCSC team,
In the last 10 days or so we can not see bigwig track in our UCSC sessions. Our local server
http://sheba-cancer.org.il (and all the track files in this server) are accessible, at least here in Israel from web browsers, but the UCSC browser does not display the tracks and complains about error in the Error column of the "Manage Custom Tracks" table. The error links states: "Could not open http://.........bw"
What can be the reason that the files are not accessible, although the local sever is up? Until 10 days ago every thing was fine.
Thnaks,
Eran
[Loading Image...
]
[Loading Image...
]<http://www.sheba.co.il/h/> [Loading Image...
] <https://yashir.sheba.co.il> [Loading Image...
] <http://www.sheba.co.il/sheba_movies> [Loading Image...
] <https://twitter.com/sheba_> [Loading Image...
] <https://www.facebook.com/SHEBA.MEDICAL?ref=ts>
=============================================================================
Topic: gene coordinates in refGene.txt
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4f7908b05cdc4797
=============================================================================
---------- 1 of 1 ----------
From: Lin Pei <***@gmail.com>
Date: Sep 30 08:14AM +0800
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1bc0107f9f7fcbd1
Hi
I have download the file refGene.txt.gz
<http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz>
from UCSC[1]
Could you please tell me in this file which two columns represent the
start and end coordinates of a gene ?
Are the first two numbers just after the sign "+/-" ?
Also, where I can find the description for what was represented by each
column ?
Thanks
Best,
[1] http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
--
Lin Pei
=============================================================================
Topic: Need help with running BLAT on CentOS
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 30 08:26AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/88c3cc6286a6975d
Hello, Aneesha.
Please run the following commands:
rpm -qa > someFileName
gcc -v
uname -a
Then please send us the file output from the first command and the output from the other two commands. You can send it directly to me if you would prefer that it doesnât go to the list.
Please contact us again at ***@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Aneesha Das [mailto:***@gmail.com]
Sent: Friday, September 26, 2014 3:37 AM
To: ***@soe.ucsc.edu
Subject: [genome] Fwd: Need help with running BLAT on CentOS
---------- Forwarded message ----------
From: Aneesha Das <***@gmail.com>
Date: Thu, Sep 25, 2014 at 8:48 PM
Subject: Re: Need help with running BLAT on CentOS
To: Jim Kent <***@soe.ucsc.edu>, ***@soe.ucsc.edu
Hi Dr.Kent,
I was trying to install the BLAT software on a machine with CentOS system as a part of the PASA pipeline. I did the following steps:
1.I uncompressed the blat folder in the PASA main directory.
2. Copied the entire PASA directory to the /usr/local/bin folder as per the instructions available in the PASA installation page (http://pasa.sourceforge.net/).
3. Logged into the blatSrc folder.
4. Obtained the MACHTYPE of the machine by typing ($MACHTYPE, x86_64-redhat-linux-gnu) and exported it.
5. Then I entered the lib directory within the blatSrc folder and typed 'make' for which the following error message was obtained.
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -c net.c
cc1: warnings being treated as errors
net.c: In function ânetAcceptingSocketFromâ:
net.c:92: error: pointer targets in passing argument 5 of âgetsockoptâ differ in signedness
/usr/include/sys/socket.h:190: note: expected âsocklen_t * __restrict__â but argument is of type âint *â
net.c: In function ânetAcceptâ:
net.c:115: error: pointer targets in passing argument 3 of âacceptâ differ in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â but argument is of type âint *â
net.c: In function ânetAcceptFromâ:
net.c:130: error: pointer targets in passing argument 3 of âacceptâ differ in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â but argument is of type âint *â
make: *** [net.o] Error 1
Kindly help me with the installation.
Regards,
Aneesha.
On Mon, Sep 8, 2014 at 5:03 AM, Jim Kent <***@soe.ucsc.edu> wrote:
Looks like you need to setenv MACHTYPE, and also do a make in the lib directory. Instructions for this should be in the README.
On Sun, Sep 7, 2014 at 7:28 AM, Aneesha Das <***@gmail.com> wrote:
Dear Dr.Kent,
I work in Dr.Saikat Chakrabarti's lab at the CSIR-Indian Institute of Chemical Biology. I have been trying to install BLAT in CentOS 5.8 server. I have downloaded the compressed version of the program (blatSrc35.zip), uncompressed the folder. But when I enter the blatSrc directory and type make (as user root), the process displays the following messages:
make[1]: Entering directory
`/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'
make[1]: *** No rule to make target `../lib//jkweb.a', needed by `blat'. Stop.
make[1]: Leaving directory `/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'
make: *** [all] Error 2
I had made a directory using the $MACHTYPE variable (x86_64-redhat-linux-gnu) in the lib directory, but the file jkweb.a could not be found anywhere.
I badly need help with the installation and running of this program (which is a part of the PASA pipeline, which I am trying to run).
Help!!
Aneesha Das.
--
=============================================================================
Topic: Genome Browser question
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
=============================================================================
---------- 1 of 1 ----------
From: "Preziosi, Morgan E" <***@pitt.edu>
Date: Sep 29 08:11PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/5720328a4bad6721
Can Genome Browser be used to create In Situ probes? If so, how?
Thanks,
Morgan
=============================================================================
Topic: A bug in table browser?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
=============================================================================
---------- 1 of 2 ----------
From: Peter Cherepanov <***@cancer.org.uk>
Date: Sep 29 03:22PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/ec9b8e9f82317cf7
When generating a table listing RefSeq or Ensemble TSS positions, table browser does makes a list of the left boundaries of the genes, regardless of the strandedness. It really should report the left boundary when strand is "+", but the right boundary when the strand is "-".
Am I missing something, or is it a bug?
In fact, when I download a complete gene table, the left boundary is always called "Tx start" and right "Tx end", which is confusing.
Many thanks in advance,
Kindest regards,
Peter
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We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you.
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Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 29 10:44AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/409cbab8ffc50cd0
Hello, Peter.
This behavior is by design. Please also see the previously-answered mailing
list question at
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/KOlZSuIpZBs/vGDfBzGjSo
8J.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions. All messages sent to that address are archived on a
publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: Peter Cherepanov [mailto:***@cancer.org.uk]
Sent: Monday, September 29, 2014 8:22 AM
To: ***@soe.ucsc.edu
Subject: [genome] A bug in table browser?
When generating a table listing RefSeq or Ensemble TSS positions, table
browser does makes a list of the left boundaries of the genes, regardless of
the strandedness. It really should report the left boundary when strand is
"+", but the right boundary when the strand is "-".
Am I missing something, or is it a bug?
In fact, when I download a complete gene table, the left boundary is always
called "Tx start" and right "Tx end", which is confusing.
Many thanks in advance,
Kindest regards,
Peter
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-named
person(s). If you are not the intended recipient, notify the sender
immediately, delete this email from your system and do not disclose or use
for any purpose.
We may monitor all incoming and outgoing emails in line with current
legislation. We have taken steps to ensure that this email and attachments
are free from any virus, but it remains your responsibility to ensure that
viruses do not adversely affect you.
Cancer Research UK
Registered charity in England and Wales (1089464), Scotland (SC041666) and
the Isle of Man (1103) A company limited by guarantee. Registered company
in England and Wales (4325234) and the Isle of Man (5713F).
Registered Office Address: Angel Building, 407 St John Street, London EC1V
4AD.
--
=============================================================================
Topic: Error message for the bisulfite-seq subtrack for the ovary sample from Roadmap Epigenomics Data Complete Collection at Wash U VizHub
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cafb1bf0a0c5789e
=============================================================================
---------- 1 of 2 ----------
From: Enrique Medina-Acosta <***@gmail.com>
Date: Sep 29 11:01AM -0300
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6f549bf27a6a4522
***@soe.ucsc.edu.
Dear UCSC Genome Browser mailing list support,
I am getting a display error message for the bisulfite-seq subtrack for the
ovary sample from Roadmap Epigenomics Data Complete Collection at Wash U
VizHub (print screen attached).
Error message at the subtrack is:" CouldnÂŽt open http://epigenomecloud.
wustl.edu/dli/roadmap/WGBS/E097.fm.bigWig"
What can I do to correct this error?
Best regards,
Enrique
Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD
<http://www.uenf.br/Uenf/Pages/CBB/LBT/?modelo=1&cod_pag=650&id=1187976458&np=&tpl=1&grupo=LBT>
.
MyCVLattes - CNPq <http://lattes.cnpq.br/0494533350878531>
MyResearcherID (ISI Web of Knowledge)
<http://www.researcherid.com/ProfileView.action?queryString=KG0UuZjN5WmTO3JU3BsaLuXY%252F2fYPzmlZ42clr%252BMEqQ%253D&Init=Yes&SrcApp=CR&returnCode=ROUTER.Unauthorized>
MyORCID <http://orcid.org/0000-0002-2529-0548>
Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos
Goytacazes, RJ, Brazil.
Tel: +55 22 2726 6758 / +55 22 2739 7086
========================================================================================
*UENF - Serviços à comunidade oriundos de pesquisa translacional
<http://www.uenf.br/portal/index.php/br/servicos/nucleo-diagnostico-investigacao-molecular.html>*
=========================================================================================
---------- 2 of 2 ----------
From: Brian Lee <***@soe.ucsc.edu>
Date: Sep 29 10:30AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/7027376a5264135d
Dear Enrique,
Thank you for using the UCSC Genome Browser and your question about a track
not displaying from the Roadmap Epigenomics Data Complete Collection Hub.
These Public Hubs are maintained externally from the UCSC Genome Browser. I
am copying this reply to the provider of the hub,***@genetics.wustl.edu,
listed on the hub.txt page:
http://vizhub.wustl.edu/VizHub/RoadmapReleaseAll.txt
Please continue any questions about the hub to that email address. It
appears that you may not have loaded this hub from the UCSC Genome Browser
Public Hubs page: http://genome.ucsc.edu/cgi-bin/hgHubConnect
A quick check of the track architecture listed there doesn't mention the
URL you shared in your screen shot (thank you for attaching that image).
Also the Bisulfite-Seq Ovary track listed from the public hub loads fine:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapReleaseAll.txt&g=hub_1623_CompRoadmapBisulfite-Seq
It also could be likely that since these are externally maintained, you may
have once loaded the hub from our site, but then the hub provider made
changes and that track URL changed since the moment you loaded the hub. You
could disconnect and reconnect to the hub, or reset your browser to solve
this problem, but please be aware that resetting would also clear your
other settings.
Since the public hub doesn't mention the http://epigenomecloud.wustl.edu site
that is causing the error for this file, I believe you likely loaded this
hub from a different source outside of the Public Hubs link, mentioned
above. In either case, emailing the hub provider, copied in this email,
should help resolve the problem.
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply ***@soe.ucsc.edu. All
messages sent to that address are archived on a publicly-accessible forum.
If your question includes sensitive data, you may send it instead to
genome-***@soe.ucsc.edu.
All the best,
Brian Lee
On Mon, Sep 29, 2014 at 7:01 AM, Enrique Medina-Acosta <
=============================================================================
Topic: Transcription factors data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
=============================================================================
---------- 1 of 1 ----------
From: Andrea Clocchiatti <***@uniud.it>
Date: Sep 28 07:35PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f7f94fa9ae9a10ce
Dear Encode consortium,
I'm Andrea Clocchiatti a postdoc interested in your great data set.
I'd like to know if theme is a tool to see all the bindings of a transcription factor (in this case Mef2A), and their corresponding genes.
If you were so kind to indicate how to identify the mef2 regulated genes in your datasets it would be very useful.
Thanking you in advance of the time dedicated and your helpfulness,
Best regards
a
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Today's topic summary
=============================================================================
Group: ***@soe.ucsc.edu
Url:
https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#!forum/genome/topics
- plotting read counts on the plus and minus strand [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
- problems to access bigwikg on our server [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
- gene coordinates in refGene.txt [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4f7908b05cdc4797
- Need help with running BLAT on CentOS [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
- Genome Browser question [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
- A bug in table browser? [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
- Error message for the bisulfite-seq subtrack for the ovary sample from Roadmap Epigenomics Data Complete Collection at Wash U VizHub [2 Updates]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cafb1bf0a0c5789e
- Transcription factors data [1 Update]
http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
=============================================================================
Topic: plotting read counts on the plus and minus strand
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/b47680c65724ec06
=============================================================================
---------- 1 of 1 ----------
From: "Yeroslaviz, Assa" <***@biochem.mpg.de>
Date: Sep 30 03:58PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1cd3dc427d323106
Hi,
I was wondering how I can plot my read counts in a strand specific way on the UCSC browser.
I would like to have the count for the gene on the plus strand to go up, while the reads mapped to the minus strand will be shown downwards.
Something like this:
[cid:B633FE69-92DD-4339-B8F0-15026C5A2445]
Is it possible to separate the two strands according to a specific parameter?
Thanks
Assa
=============================================================================
Topic: problems to access bigwikg on our server
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f7633c36dce1b89d
=============================================================================
---------- 1 of 1 ----------
From: "Dr. Eyal Eran" <***@sheba.health.gov.il>
Date: Sep 30 03:06PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/a2cc165e6036fb8e
Dear UCSC team,
In the last 10 days or so we can not see bigwig track in our UCSC sessions. Our local server
http://sheba-cancer.org.il (and all the track files in this server) are accessible, at least here in Israel from web browsers, but the UCSC browser does not display the tracks and complains about error in the Error column of the "Manage Custom Tracks" table. The error links states: "Could not open http://.........bw"
What can be the reason that the files are not accessible, although the local sever is up? Until 10 days ago every thing was fine.
Thnaks,
Eran
[Loading Image...
][Loading Image...
]<http://www.sheba.co.il/h/> [Loading Image...
] <https://yashir.sheba.co.il> [Loading Image...
] <http://www.sheba.co.il/sheba_movies> [Loading Image...
] <https://twitter.com/sheba_> [Loading Image...
] <https://www.facebook.com/SHEBA.MEDICAL?ref=ts>=============================================================================
Topic: gene coordinates in refGene.txt
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4f7908b05cdc4797
=============================================================================
---------- 1 of 1 ----------
From: Lin Pei <***@gmail.com>
Date: Sep 30 08:14AM +0800
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/1bc0107f9f7fcbd1
Hi
I have download the file refGene.txt.gz
<http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz>
from UCSC[1]
Could you please tell me in this file which two columns represent the
start and end coordinates of a gene ?
Are the first two numbers just after the sign "+/-" ?
Also, where I can find the description for what was represented by each
column ?
Thanks
Best,
[1] http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
--
Lin Pei
=============================================================================
Topic: Need help with running BLAT on CentOS
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/6397885d9d8f22bd
=============================================================================
---------- 1 of 1 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 30 08:26AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/88c3cc6286a6975d
Hello, Aneesha.
Please run the following commands:
rpm -qa > someFileName
gcc -v
uname -a
Then please send us the file output from the first command and the output from the other two commands. You can send it directly to me if you would prefer that it doesnât go to the list.
Please contact us again at ***@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
From: Aneesha Das [mailto:***@gmail.com]
Sent: Friday, September 26, 2014 3:37 AM
To: ***@soe.ucsc.edu
Subject: [genome] Fwd: Need help with running BLAT on CentOS
---------- Forwarded message ----------
From: Aneesha Das <***@gmail.com>
Date: Thu, Sep 25, 2014 at 8:48 PM
Subject: Re: Need help with running BLAT on CentOS
To: Jim Kent <***@soe.ucsc.edu>, ***@soe.ucsc.edu
Hi Dr.Kent,
I was trying to install the BLAT software on a machine with CentOS system as a part of the PASA pipeline. I did the following steps:
1.I uncompressed the blat folder in the PASA main directory.
2. Copied the entire PASA directory to the /usr/local/bin folder as per the instructions available in the PASA installation page (http://pasa.sourceforge.net/).
3. Logged into the blatSrc folder.
4. Obtained the MACHTYPE of the machine by typing ($MACHTYPE, x86_64-redhat-linux-gnu) and exported it.
5. Then I entered the lib directory within the blatSrc folder and typed 'make' for which the following error message was obtained.
gcc -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -c net.c
cc1: warnings being treated as errors
net.c: In function ânetAcceptingSocketFromâ:
net.c:92: error: pointer targets in passing argument 5 of âgetsockoptâ differ in signedness
/usr/include/sys/socket.h:190: note: expected âsocklen_t * __restrict__â but argument is of type âint *â
net.c: In function ânetAcceptâ:
net.c:115: error: pointer targets in passing argument 3 of âacceptâ differ in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â but argument is of type âint *â
net.c: In function ânetAcceptFromâ:
net.c:130: error: pointer targets in passing argument 3 of âacceptâ differ in signedness
/usr/include/sys/socket.h:214: note: expected âsocklen_t * __restrict__â but argument is of type âint *â
make: *** [net.o] Error 1
Kindly help me with the installation.
Regards,
Aneesha.
On Mon, Sep 8, 2014 at 5:03 AM, Jim Kent <***@soe.ucsc.edu> wrote:
Looks like you need to setenv MACHTYPE, and also do a make in the lib directory. Instructions for this should be in the README.
On Sun, Sep 7, 2014 at 7:28 AM, Aneesha Das <***@gmail.com> wrote:
Dear Dr.Kent,
I work in Dr.Saikat Chakrabarti's lab at the CSIR-Indian Institute of Chemical Biology. I have been trying to install BLAT in CentOS 5.8 server. I have downloaded the compressed version of the program (blatSrc35.zip), uncompressed the folder. But when I enter the blatSrc directory and type make (as user root), the process displays the following messages:
make[1]: Entering directory
`/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'
make[1]: *** No rule to make target `../lib//jkweb.a', needed by `blat'. Stop.
make[1]: Leaving directory `/hpchome1/saikat/SOFTWARE/EVM/PASA_r20140417/blatSrc/blat'
make: *** [all] Error 2
I had made a directory using the $MACHTYPE variable (x86_64-redhat-linux-gnu) in the lib directory, but the file jkweb.a could not be found anywhere.
I badly need help with the installation and running of this program (which is a part of the PASA pipeline, which I am trying to run).
Help!!
Aneesha Das.
--
=============================================================================
Topic: Genome Browser question
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/f4402290e94a695
=============================================================================
---------- 1 of 1 ----------
From: "Preziosi, Morgan E" <***@pitt.edu>
Date: Sep 29 08:11PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/5720328a4bad6721
Can Genome Browser be used to create In Situ probes? If so, how?
Thanks,
Morgan
=============================================================================
Topic: A bug in table browser?
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/3dcc96a3fd1fd3a4
=============================================================================
---------- 1 of 2 ----------
From: Peter Cherepanov <***@cancer.org.uk>
Date: Sep 29 03:22PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/ec9b8e9f82317cf7
When generating a table listing RefSeq or Ensemble TSS positions, table browser does makes a list of the left boundaries of the genes, regardless of the strandedness. It really should report the left boundary when strand is "+", but the right boundary when the strand is "-".
Am I missing something, or is it a bug?
In fact, when I download a complete gene table, the left boundary is always called "Tx start" and right "Tx end", which is confusing.
Many thanks in advance,
Kindest regards,
Peter
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Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
---------- 2 of 2 ----------
From: "Steve Heitner" <***@soe.ucsc.edu>
Date: Sep 29 10:44AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/409cbab8ffc50cd0
Hello, Peter.
This behavior is by design. Please also see the previously-answered mailing
list question at
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/KOlZSuIpZBs/vGDfBzGjSo
8J.
Please contact us again at ***@soe.ucsc.edu if you have any further
questions. All messages sent to that address are archived on a
publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genome-***@soe.ucsc.edu.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: Peter Cherepanov [mailto:***@cancer.org.uk]
Sent: Monday, September 29, 2014 8:22 AM
To: ***@soe.ucsc.edu
Subject: [genome] A bug in table browser?
When generating a table listing RefSeq or Ensemble TSS positions, table
browser does makes a list of the left boundaries of the genes, regardless of
the strandedness. It really should report the left boundary when strand is
"+", but the right boundary when the strand is "-".
Am I missing something, or is it a bug?
In fact, when I download a complete gene table, the left boundary is always
called "Tx start" and right "Tx end", which is confusing.
Many thanks in advance,
Kindest regards,
Peter
NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for the above-named
person(s). If you are not the intended recipient, notify the sender
immediately, delete this email from your system and do not disclose or use
for any purpose.
We may monitor all incoming and outgoing emails in line with current
legislation. We have taken steps to ensure that this email and attachments
are free from any virus, but it remains your responsibility to ensure that
viruses do not adversely affect you.
Cancer Research UK
Registered charity in England and Wales (1089464), Scotland (SC041666) and
the Isle of Man (1103) A company limited by guarantee. Registered company
in England and Wales (4325234) and the Isle of Man (5713F).
Registered Office Address: Angel Building, 407 St John Street, London EC1V
4AD.
--
=============================================================================
Topic: Error message for the bisulfite-seq subtrack for the ovary sample from Roadmap Epigenomics Data Complete Collection at Wash U VizHub
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/cafb1bf0a0c5789e
=============================================================================
---------- 1 of 2 ----------
From: Enrique Medina-Acosta <***@gmail.com>
Date: Sep 29 11:01AM -0300
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/6f549bf27a6a4522
***@soe.ucsc.edu.
Dear UCSC Genome Browser mailing list support,
I am getting a display error message for the bisulfite-seq subtrack for the
ovary sample from Roadmap Epigenomics Data Complete Collection at Wash U
VizHub (print screen attached).
Error message at the subtrack is:" CouldnÂŽt open http://epigenomecloud.
wustl.edu/dli/roadmap/WGBS/E097.fm.bigWig"
What can I do to correct this error?
Best regards,
Enrique
Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD
<http://www.uenf.br/Uenf/Pages/CBB/LBT/?modelo=1&cod_pag=650&id=1187976458&np=&tpl=1&grupo=LBT>
.
MyCVLattes - CNPq <http://lattes.cnpq.br/0494533350878531>
MyResearcherID (ISI Web of Knowledge)
<http://www.researcherid.com/ProfileView.action?queryString=KG0UuZjN5WmTO3JU3BsaLuXY%252F2fYPzmlZ42clr%252BMEqQ%253D&Init=Yes&SrcApp=CR&returnCode=ROUTER.Unauthorized>
MyORCID <http://orcid.org/0000-0002-2529-0548>
Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos
Goytacazes, RJ, Brazil.
Tel: +55 22 2726 6758 / +55 22 2739 7086
========================================================================================
*UENF - Serviços à comunidade oriundos de pesquisa translacional
<http://www.uenf.br/portal/index.php/br/servicos/nucleo-diagnostico-investigacao-molecular.html>*
=========================================================================================
---------- 2 of 2 ----------
From: Brian Lee <***@soe.ucsc.edu>
Date: Sep 29 10:30AM -0700
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/7027376a5264135d
Dear Enrique,
Thank you for using the UCSC Genome Browser and your question about a track
not displaying from the Roadmap Epigenomics Data Complete Collection Hub.
These Public Hubs are maintained externally from the UCSC Genome Browser. I
am copying this reply to the provider of the hub,***@genetics.wustl.edu,
listed on the hub.txt page:
http://vizhub.wustl.edu/VizHub/RoadmapReleaseAll.txt
Please continue any questions about the hub to that email address. It
appears that you may not have loaded this hub from the UCSC Genome Browser
Public Hubs page: http://genome.ucsc.edu/cgi-bin/hgHubConnect
A quick check of the track architecture listed there doesn't mention the
URL you shared in your screen shot (thank you for attaching that image).
Also the Bisulfite-Seq Ovary track listed from the public hub loads fine:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapReleaseAll.txt&g=hub_1623_CompRoadmapBisulfite-Seq
It also could be likely that since these are externally maintained, you may
have once loaded the hub from our site, but then the hub provider made
changes and that track URL changed since the moment you loaded the hub. You
could disconnect and reconnect to the hub, or reset your browser to solve
this problem, but please be aware that resetting would also clear your
other settings.
Since the public hub doesn't mention the http://epigenomecloud.wustl.edu site
that is causing the error for this file, I believe you likely loaded this
hub from a different source outside of the Public Hubs link, mentioned
above. In either case, emailing the hub provider, copied in this email,
should help resolve the problem.
Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply ***@soe.ucsc.edu. All
messages sent to that address are archived on a publicly-accessible forum.
If your question includes sensitive data, you may send it instead to
genome-***@soe.ucsc.edu.
All the best,
Brian Lee
On Mon, Sep 29, 2014 at 7:01 AM, Enrique Medina-Acosta <
=============================================================================
Topic: Transcription factors data
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/t/acf0af1a9ae5c42d
=============================================================================
---------- 1 of 1 ----------
From: Andrea Clocchiatti <***@uniud.it>
Date: Sep 28 07:35PM
Url: http://groups.google.com/a/soe.ucsc.edu/group/genome/msg/f7f94fa9ae9a10ce
Dear Encode consortium,
I'm Andrea Clocchiatti a postdoc interested in your great data set.
I'd like to know if theme is a tool to see all the bindings of a transcription factor (in this case Mef2A), and their corresponding genes.
If you were so kind to indicate how to identify the mef2 regulated genes in your datasets it would be very useful.
Thanking you in advance of the time dedicated and your helpfulness,
Best regards
a
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