Here's what I see when I try to create a docker container:
> 79.27 + checkDownloadUdr
> 79.27 + [[ ! -f /usr/local/bin/udr ]]
> 79.27 + echo2 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr'
> 79.27 + command echo '|' 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr'
> 79.27 + echo '|' 'Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr'
> 79.27 | Downloading download-tool udr (UDP-based rsync with multiple streams) to /usr/local/bin/udr
> 79.27 + waitKey
> 79.27 + echo
> 79.27
> 79.27 + downloadFile
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr
> 79.27 + url=
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr
> 79.27 + which wget
> 79.27 + wget -nv
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr -O -
> 80.19 2025-02-20 18:03:31 URL:
http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/udr [2840528/2840528] -> "-" [1]
> 80.19 + chmod a+x /usr/local/bin/udr
> 80.19 + '[' '!' -f /usr/local/apache/cgiInstallComplete.flag ']'
> 80.19 + '[' -f /usr/local/apache ']'
> 80.19 + '[' -d /usr/local/apache -a linux '!=' OSX ']'
> 80.19 + mysqlDbSetup
> 80.19 + echo2
> 80.19 + command echo '|'
> 80.19 + echo '|'
> 80.19 |
> 80.19 + echo2 Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 + command echo '|' Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 + echo '|' Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 | Creating Mysql databases customTrash, hgTemp and hgcentral
> 80.19 + waitKey
> 80.19 + echo
> 80.19
> 80.19 + mysql -e 'CREATE DATABASE IF NOT EXISTS customTrash;'
> 80.20 + mysql -e 'CREATE DATABASE IF NOT EXISTS hgcentral;'
> 80.21 + mysql -e 'CREATE DATABASE IF NOT EXISTS hgTemp;'
> 80.22 + mysql -e 'CREATE DATABASE IF NOT EXISTS hgFixed;'
> 80.22 + updateBlatServers
> 80.22 + echo2 Creating or updating the BLAT servers table
> 80.22 + command echo '|' Creating or updating the BLAT servers table
> 80.22 + echo '|' Creating or updating the BLAT servers table
> 80.22 | Creating or updating the BLAT servers table
> 80.22 + downloadFile
http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql
> 80.22 + url=
http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql
> 80.22 + which wget
> 80.22 + mysql hgcentral
> 80.23 + wget -nv
http://hgdownload.soe.ucsc.edu/admin/hgcentral.sql -O -
> 80.37 ERROR at line 1: Unknown command '\-'.
> 80.44 Cannot write to ‘-’ (Broken pipe).
> 80.44 + exitHandler 1 1
> 80.44 + '[' 1 == 100 -o 1 == 0 ']'
> 80.44 + echo Exit error 1 occurred on line 1
> 80.44 Exit error 1 occurred on line 1
> 80.44 + echo The UCSC Genome Browser installation script exited with an error.
> 80.44 The UCSC Genome Browser installation script exited with an error.
> 80.44 + echo Please contact us at
genome...@soe.ucsc.edu and send us an output log
> 80.44 Please contact us at
genome...@soe.ucsc.edu and send us an output log
> 80.44 + echo of the command prefixed with '"bash -x",' e.g.
> 80.44 of the command prefixed with "bash -x", e.g.
> 80.44 + echo 'bash -x browserSetup.sh install 2>&1 > install.log'
> 80.44 bash -x browserSetup.sh install 2>&1 > install.log
On 2/19/2025 1:40 PM, 'Jairo Navarro Gonzalez' via UCSC Genome Browser Mirror-Specific Support wrote:
> Hello,
>
> Thank you for using the UCSC Genome Browser and reporting your issues.
>
> Could you run the following command and then send us the output to help debug the issues?
>
> bash -x browserSetup.sh install 2>&1 > install.log
>
> We need the last few lines with the error to debug the issues.
>
> If you have any further questions, please reply to
genome...@soe.ucsc.edu <mailto:
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 <mailto:
genom...@soe.ucsc.edu>.
>
> Jairo Navarro
> UCSC Genome Browser
>
>
> On Wed, Feb 19, 2025 at 9:36 AM 'McCully, Dwayne (NIH/NIAMS) [C]' via UCSC Genome Browser Mirror-Specific Support <
genome...@soe.ucsc.edu <mailto:
genome...@soe.ucsc.edu>> wrote:
>
> Hello Genome Mirror Support,____
>
> __ __
>
> When running the update I got the following error and the update stopped. ____
>
> Please advise on what to do next?____
>
> __ __
>
> __ __
>
> sent 55,599 bytes received 1,084,157 bytes 207,228.36 bytes/sec____
>
> total size is 261,114,875 speedup is 229.10____
>
> | Creating or updating the BLAT servers table____
>
> ERROR at line 1: Unknown command '\-'.____
>
> Cannot write to '-' (Broken pipe).____
>
> Exit error 1 occurred on line 1____
>
> The UCSC Genome Browser installation script exited with an error.____
>
> Please contact us at
genome...@soe.ucsc.edu <mailto:
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____
>
> __ __
>
> __ __
>
> Dwayne McCully____
>
> NIAMS, NIH, SITB____
>
> Contractor____
>
> --
>
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> To view this discussion visit
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>
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>
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> To unsubscribe from this group and stop receiving emails from it, send an email to
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> To view this discussion visit
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--
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL:
(+1) 301-435-2986
Email:
hoov...@hpc.nih.gov