Problem in running blatsrc35 on suse linux

[qanita khalid]

Hi,
I was trying to install blat on machine with suse linux. I did the following steps in blat installation.

1. First, I download the latest version of blat from ucsc genome browser.

2. Uncompressed the blat folder in root folder of system.

3. Create blatsrc directory and moved in.

4. Obtained machine type by typing 'echo $Machtype'. That's return machine btype which is x86_64 -suse-linux.

5. Now , i temprory export the machine type, not creating bash file.

6. Not creating the directory 'lib/$MACHTYPE', because that was already exists.

7. I want to create directory in 'bin', where all executables go, but that was not created by system easily. After i create it, but that was not visible in bin folder.

8.. Now when command 'make' run on system then i got following errors..




make[1]: Entering directory '/usr/local/blat/blatSrc/jkOwnLib'
make[1]: '../lib/x86_64-suse-linux/jkOwnLib.a' is up to date.
make[1]: Leaving directory '/usr/local/blat/blatSrc/jkOwnLib'
cd blat && make
make[1]: Entering directory '/usr/local/blat/blatSrc/blat'
gcc -O -g  -o /home/eglab/bin/x86_64-suse-linux/blat blat.o ../lib/x86_64-suse-linux/jkOwnLib.a ../lib/x86_64-suse-linux/jkweb.a   -pthread -lm
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot open output file /home/eglab/bin/x86_64-suse-linux/blat: No such file or directory
collect2: error: ld returned 1 exit status
makefile:10: recipe for target 'blat' failed
make[1]: *** [blat] Error 1
make[1]: Leaving directory '/usr/local/blat/blatSrc/blat'
makefile:2: recipe for target 'all' failed
make: *** [all] Error 2
eglab@linux-5pj5:/usr/local/blat/blatSrc>





Kindly help me with installation..




Best Regards

Qanta Khalid

[Cath Tyner]

Hello Qanta,

If you are trying to do this build as the 'root' user, that could be causing some problems - we don't advise doing this, and it isn't necessary. Other troubleshooting steps to review can be found in our mailing list archive:

*Previously answered mailing list questions* that may be helpful:

* https://groups.google.com/a/soe.ucsc.edu/d/msg/genome-mirror/4KB5HJATo_U/vqmcF7FhAwAJ

* https://groups.google.com/a/soe.ucsc.edu/d/msg/genome-mirror/0xYKQUe34Kg/U0tCfVLPavMJ

* https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/rxeus8PD1yc/wnxFjiwUHtsJ 

(solution: changed MACHTYPE with dashes in it, removed dashes)

Please note that BLAT source and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the "Kent Informatics website":http://www.kentinformatics.com/.

BLAT source

http://hgwdev.cse.ucsc.edu/~kent/src/?C=M;O=D

Current version:

blatSrc36.zip 05-Nov-2014 19:24 3.1M

Build instructions

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob_plain;f=src/product/README.building.source

BLAT executables

http://hgdownload.soe.ucsc.edu/admin/exe/ 

BLAT Suite Program Specifications and User Guide

http://genome.ucsc.edu/goldenPath/help/blatSpec.html

As you move forward, please feel free to respond to this forum at any time for further assistance. If you can reply with the source you are using, and which instructions you are following, we may be able to provide further assistance. 

Also, if you do find the solution, it is always very helpful to reply to this forum with details that may help other users!

Thank you for contacting the UCSC Genome Browser support team. 

​

Please send new and follow-up questions to one of our mailing lists below:

  * Post to the Public Help Forum: E

mail 

gen...@soe.ucsc.edu

​ or search the Public Archives

​  * Post to the Mirror Help Forum: Email

 genome...@soe.ucsc.edu 

or search the Mirror Archives​

​  * Confidential/private help: Email

 genom...@soe.ucsc.edu

Join us on Social Media! Facebook, Twitter, Wordpress Blog, YouTube

UCSC Genome Browser Announcements List (for new data & software)

Request on-site training & workshops at your institution

​Enjoy,​

Cath

. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CABpUMONBZo8nAb%2BYY2Jd5WcjGhfNbnO9aP6PW5%3DHng_E1_OVDQ%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.