mirror rnm39

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Chen, John (IT)

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May 8, 2024, 9:09:49 AMMay 8
to genome...@soe.ucsc.edu
Hi, 

I am trying to mirror rnm39 for a researcher and is getting the following error message.  Am i doing something wrong with this track?

BTW - I have already created the symlink of /var/lib/mysql to a large NFS share already and able to mirror hg38, , rn6, mm10, and rn7



|
| Downloading databases rnm39 plus hgFixed/proteome/go from the UCSC download server
|
| Determining download file size... please wait...
| Downloading rnm39 plus GenBank and RefSeq tables
rsync: [sender] change_dir "/rnm39" (in mysql) failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1823) [Receiver=3.2.3]
| Required space in /var/lib/mysql: 0 GB
Exit error 23 occurred on line 1
The UCSC Genome Browser installation script exited with an error.
Please contact us at genome...@soe.ucsc.edu and send us an output log
of the command prefixed with "bash -x", e.g.
bash -x browserSetup.sh install 2>&1 > install.log



This is the output of the install.log

+ set -u -e -o pipefail
+ export LANG=C
+ LANG=C
+ trap 'exitHandler $? $LINENO' EXIT
+ APACHEDIR=/usr/local/apache
+ HTDOCDIR=/usr/local/apache/htdocs
+ CGIBINDIR=/usr/local/apache/cgi-bin
+ TRASHDIR=/usr/local/apache/trash
+ MYSQLDIR=/var/lib/mysql
+ MYSQLADMIN=mysqladmin
+ MYSQLUSER=mysql
+ MYSQL=mysql
+ SET_MYSQL_ROOT=0
+ GBDBDIR=/gbdb
+ SEDINPLACE='sed -ri'
+ RSYNC=rsync
+ RSYNCOPTS=
+ COMPLETEFLAG=/usr/local/apache/cgiInstallComplete.flag
+ BUILDEXT=0
+ BUILDKENT=0
+ ONLYGENOMES=0
+ set +e
+ read -r -d '' APACHE_CONFIG_STR
+ read -r -d '' HG_CONF_STR
+ read -r -d '' HELP_STR
+ set -e
+ [[ '' != '' ]]
+ trap errorHandler ERR
+ [[ 2 -eq 0 ]]
+ getopts :baeut:hof opt
+ shift 0
++ uname
+ unameStr=Linux
+ DIST=none
+ [[ Linux == MINGW32_NT* ]]
+ [[ Linux == Darwin* ]]
+ [[ Linux == Linux* ]]
+ OS=linux
+ '[' -f /etc/debian_version ']'
+ [[ -f /etc/redhat-release ]]
+ DIST=redhat
++ cat /etc/redhat-release
+ VER='Red Hat Enterprise Linux release 9.3 (Plow)'
+ APACHECONF=/etc/httpd/conf.d/001-browser.conf
+ APACHEUSER=apache
+ VERNUM=0
+ '[' -f /etc/system-release-cpe ']'
++ cut /etc/system-release-cpe -d: -f5
+ VERNUM=9
+ '[' -f /etc/os-release ']'
++ cat /etc/os-release
++ grep VERSION_ID
++ cut -d= -f2
++ tr -d '"'
+ VERNUM=9.3
+ '[' redhat == none ']'
+ lastArg=rnm39
+ [[ 2 -gt 1 ]]
+ [[ r == \- ]]
+ [[ r == \- ]]
+ uname -m
+ grep -vq _64
+ [[ 0 != \0 ]]
+ '[' mirror == install ']'
+ '[' mirror == minimal ']'
+ '[' mirror == mirror ']'
+ downloadGenomes rnm39
+ DBS=rnm39
+ GENBANKTBLS=
+ '[' rnm39 == '' ']'
+ echo2
+ command echo '|'
|
+ echo2 Downloading databases rnm39 plus hgFixed/proteome/go from the UCSC download server
+ command echo '|' Downloading databases rnm39 plus hgFixed/proteome/go from the UCSC download server
| Downloading databases rnm39 plus hgFixed/proteome/go from the UCSC download server
+ echo2
+ command echo '|'
+ echo2 Determining download file size... please wait...
+ command echo '|' Determining download file size... please wait...
| Determining download file size... please wait...
+ '[' 0 == 0 ']'
+ [[ rnm39 =~ hg|mm|rn3|rn4|sacCer|dm3|danRer3|ce6 ]]
+ echo2 Downloading rnm39 plus GenBank and RefSeq tables
+ command echo '|' Downloading rnm39 plus GenBank and RefSeq tables
| Downloading rnm39 plus GenBank and RefSeq tables
+ MYSQLDBS=rnm39
+ GENBANKTBLS='author cell description development gbCdnaInfo gbExtFile gbLoaded                          gbMiscDiff gbSeq gbWarn geneName imageClo
ne keyword library                          mrnaClone organism productName refLink refSeqStatus                          refSeqSummary sex source t
issue'
+ set -f
+ for db in $MYSQLDBS
+ awk '{ sum += $1 } END { print "| Required space in /var/lib/mysql:", sum/1000000000, "GB" }'
+ rsync -avn hgdownload.soe.ucsc.edu::mysql/rnm39/ /var/lib/mysql/rnm39/
+ grep '^total size'
+ cut '-d ' -f4
+ tr -d ', '
rsync: [sender] change_dir "/rnm39" (in mysql) failed: No such file or directory (2)
+ for db in $MYSQLDBS
+ awk '{ sum += $1 } END { print "| Required space in /var/lib/mysql:", sum/1000000000, "GB" }'
+ rsync -avn hgdownload.soe.ucsc.edu::mysql/rnm39/ /var/lib/mysql/rnm39/
+ grep '^total size'
+ cut '-d ' -f4
+ tr -d ', '
rsync: [sender] change_dir "/rnm39" (in mysql) failed: No such file or directory (2)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1823) [Receiver=3.2.3]
| Required space in /var/lib/mysql: 0 GB
+ exitHandler 23 1
+ '[' 23 == 100 -o 23 == 0 ']'
+ echo Exit error 23 occurred on line 1
Exit error 23 occurred on line 1
+ echo The UCSC Genome Browser installation script exited with an error.
The UCSC Genome Browser installation script exited with an error.
+ echo Please contact us at genome...@soe.ucsc.edu and send us an output log
Please contact us at genome...@soe.ucsc.edu and send us an output log
+ echo of the command prefixed with '"bash -x",' e.g.
of the command prefixed with "bash -x", e.g.
+ echo 'bash -x browserSetup.sh install 2>&1 > install.log'
bash -x browserSetup.sh install 2>&1 > install.log

Jairo Navarro Gonzalez

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May 10, 2024, 9:51:38 AMMay 10
to Chen, John (IT), genome...@soe.ucsc.edu

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The issue is that you are trying to download the rnm39 genome, which does not exist in the UCSC database. You are most likely trying to access the mm39 assembly for mouse. You may want to change the font on your web browser or terminal so that the two letters 'rn' look different from the single letter m.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu.
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 genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser


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Chen, John (IT)

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May 10, 2024, 1:23:51 PMMay 10
to Jairo Navarro Gonzalez, genome...@soe.ucsc.edu

Hi Jairo,

 

Thanks for the feedback.  I have another question from the lab member.  

 

One user has mentioned that moving to a new mirror will lose all their saved sessions (they have 104). Is there any way to transfer over the sessions?

 

 

 

Thanks,

John Chen

 

 

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Friday, May 10, 2024 9:51 AM
To: Chen, John (IT) <John...@nyulangone.org>
Cc: genome...@soe.ucsc.edu
Subject: Re: [genome-mirror] mirror rnm39

 

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[EXTERNAL]

Luis Nassar

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May 29, 2024, 7:37:05 PMMay 29
to Chen, John (IT), Jairo Navarro Gonzalez, genome...@soe.ucsc.edu

Hello.

Moving to a new mirror while retaining sessions is doable but not entirely straightforward. Let us know if you wish to proceed and we can help out further, but I'll share the general steps below. Keep in mind there are limited cases of this being done so there may be some trial and error. Also, it would be highly encouraged that the original mirror is kept around while the new one is configured to ensure the transfer is successful.

You would have to copy the following databases and files:

  • hgcentral tables:
    • namedSessionDb
    • gbMembers
    • hubStatus
  • Saved session custom track databases (assuming sessionDataDbPrefix=customData as we have; note that these are entire databases not just tables. Your own mirror may have a different specified in your configuration file):
    • customData01
    • customData02
    • ...
    • customData31
  • Saved session custom track files (assuming sessionDataDir=/userdata/sessions)
    • /userdata/sessions (or whatever sessionDataDir is set to)

You may also find this previously answered question insightful (https://groups.google.com/a/soe.ucsc.edu/g/genome-mirror/c/JqfDd7DLxp0/m/xIbpFQ_dAAAJ).

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute


Chen, John (IT)

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May 29, 2024, 9:39:07 PMMay 29
to Luis Nassar, Jairo Navarro Gonzalez, genome...@soe.ucsc.edu, gen...@soe.ucsc.edu

Hi Lou,

 

I will give it a try tomorrow with the steps you provided.  If unsuccessfully, do you think we could do a remote session to get me going?    I recall when I setup the first instance of the genome browser someone very technical from ucsc.edu assisted and got us going and had no issue since then.

 

Thanks,

John Chen

 

 

From: Luis Nassar <lrna...@ucsc.edu>
Sent: Wednesday, May 29, 2024 7:36 PM
To: Chen, John (IT) <John...@nyulangone.org>
Cc: Jairo Navarro Gonzalez <jnav...@ucsc.edu>; genome...@soe.ucsc.edu
Subject: Re: [genome-mirror] mirror rnm39

 

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Gerardo Perez

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Jun 11, 2024, 8:52:05 PMJun 11
to Chen, John (IT), genome...@soe.ucsc.edu, gen...@soe.ucsc.edu

Hello, John.

Unfortunately, we don’t schedule video calls. We did want to check in with you to see if you were able to move to a new mirror and retain your sessions. Let us know if you are still having problems or if you have any questions.

Gerardo Perez
UCSC Genomics Institute


Chen, John (IT)

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Jun 12, 2024, 11:32:45 AMJun 12
to Gerardo Perez, genome...@soe.ucsc.edu, gen...@soe.ucsc.edu

Hi Gerardo,

 

I gave it a try a few time and doesn’t see to get it working.  Not sure what I did incorrectly .. I will see if I could capture all the command I ran tomorrow again..

 

Thanks,

John Chen

 

 

From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Tuesday, June 11, 2024 8:52 PM
To: Chen, John (IT) <John...@nyulangone.org>
Cc: genome...@soe.ucsc.edu; gen...@soe.ucsc.edu
Subject: Re: [genome-mirror] mirror rnm39

 

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