UCSC visualization of TOGA results

Liu Xiaojie

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May 30, 2024, 11:27:51 AMMay 30

to genome...@soe.ucsc.edu

Dear UCSC team,

I am Xiaojie Liu from Nanjing Normal University. I am trying to visualize the TOGA (Integrating gene annotation with orthology inference at scale." Science 380.6643 (2023): eabn3107) output data with UCSC genomebrowser.

I can visualize the TOGA output data(xx.chain et al. ) with UCSC online version primarily without any problem. And the further analysis of the data needs the local install of UCSC browser.

I installed UCSC with GBIC box and I could get the familiar desktop with 127.0.0.1. However the instruction of TOGA seems that I have to modify the kent/makefile at the beginning of installation.

(https://github.com/hillerlab/TOGA/tree/master/ucsc_browser_visualisation). Since the GBIC installation looks like a "black box", I am wondering is it mandatory for me to install the UCSC step by step manually? Or there is a chance that I can use GBIC box to visualize the data.

Last, I am not really skilled in scripts and the instruction of the manual install on the website of UCSC seems too complex for me. Do you have some simple step by step installation instruction if I have to install that manully.

Thanks for your kind help.

Best,

Xiaojie

祝好，

刘晓杰

南京师范大学，江苏省南京市栖霞区学林路2号

Michael Hiller

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Jun 3, 2024, 12:09:30 PMJun 3

to Liu Xiaojie, genome...@soe.ucsc.edu

Hi Xiaojie,

can you pls check if your GBIC has these files

./hg/hgc/togaClick.c

./hg/hgc/togaClick.h

that handle the TOGA visualization?

Maybe they are not included in the GBIC build?

Thx a lot

- Michael

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Michael Hiller, PhD

Professor of Comparative Genomics
LOEWE Centre for Translational Biodiversity Genomics,
Senckenberg Society for Nature Research & Goethe University,

Frankfurt am Main, Germany

Michael Hiller

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Jun 5, 2024, 7:51:03 AMJun 5

to Liu Xiaojie, genome...@soe.ucsc.edu

On 5. Jun 2024, at 03:44, Liu Xiaojie <liuxia...@hotmail.com> wrote:

Dear Michael,
In the GBIC install pack (browserSetup.sh) line 661-691, they download and make compile of kent/src source code and the togaClick.c &togaClick.h should be in the source code. However, I can not find it after the installation. As I understand, the main installation directory is /usr/local/apache/, and there are only 4 folders /cig-bin/, /htdocs/, /trash/, and userdata/.

those directories will contain the cgi binaries after compiling the code (and html files etc).

I can not find the togaClick.c nor togaClick.h in the folder. If I try to find them in the server with 'locate', the 2 file I found are in the folder (see attached) where I compile kent/src by myself for which I tried to install UCSC step by step manually and ends in failure.
Whats your suggestion? Should I try to install UCSC manually or the GBIC can be used if I modify some code?

The UCSC folks may pls comment on which code version is inside the GBIC. I unfortunately have no experience with this, as we have a local installation of the code.

Thx a lot

- Michael

Thanks for your patient help.
Best
Xiaojie
<image.png>

发件人: Michael Hiller <michael...@senckenberg.de>
发送时间: 2024年6月3日 15:22
收件人: Liu Xiaojie <liuxia...@hotmail.com>
抄送: genome...@soe.ucsc.edu <genome...@soe.ucsc.edu>
主题: Re: [genome-mirror] UCSC visualization of TOGA results

<browserSetup.sh>

Liu Xiaojie

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Jun 5, 2024, 7:51:07 AMJun 5

to Michael Hiller, genome...@soe.ucsc.edu

Dear Michael,

In the GBIC install pack (browserSetup.sh) line 661-691, they download and make compile of kent/src source code and the togaClick.c &togaClick.h should be in the source code. However, I can not find it after the installation. As I understand, the main installation directory is /usr/local/apache/, and there are only 4 folders /cig-bin/, /htdocs/, /trash/, and userdata/. I can not find the togaClick.c nor togaClick.h in the folder. If I try to find them in the server with 'locate', the 2 file I found are in the folder (see attached) where I compile kent/src by myself for which I tried to install UCSC step by step manually and ends in failure.

Whats your suggestion? Should I try to install UCSC manually or the GBIC can be used if I modify some code?

Thanks for your patient help.

Best

Xiaojie

发件人: Michael Hiller <michael...@senckenberg.de>
发送时间: 2024年6月3日 15:22
收件人: Liu Xiaojie <liuxia...@hotmail.com>
抄送: genome...@soe.ucsc.edu <genome...@soe.ucsc.edu>
主题: Re: [genome-mirror] UCSC visualization of TOGA results

browserSetup.sh

Maximilian Haeussler

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Jun 5, 2024, 12:15:39 PMJun 5

to Michael Hiller, Liu Xiaojie, genome...@soe.ucsc.edu

In the GBIC install pack (browserSetup.sh) line 661-691, they download and make compile of kent/src source code and the togaClick.c &togaClick.h should be in the source code.

Hi Xiaojie,

the "install" option installs the pre-built binaries. That's probably what you want to do.

The "dev" option sets up the source code, but for a mirror local installation, you don't need that.