Installation issues

[Stiles, Morgaine]

Hello there,

I'm very new to using LINUX and am trying to install BLAT on a LINUX Mint 17.3 OS (for my final year undergrad project, hence the lack in background)

My workflow so far

Download BLAT and unzip

Then in ~

echo $MACHTYPE = x86_64-pc-linux-gnu

mkdir -p bin/$MACHTYPE

PATH=$PATH:~/bin/$MACHTYPE

cd /lib

sudo mkdir $MACHTYPE

sudo apt-get update && sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev

Navigate back to the blatSrc directory and command "make" works until

ar: /jkweb.a: Permission denied
make[1]: *** [/jkweb.a] Error 1
make[1]: Leaving directory `/home/beebylab/Apollo-2.0.6/blatSrc/lib'
make: *** [all] Error 2

I attach the full readout.

I'm not sure what the issue is, or how to address it.

Thank you

Morgaine

[Hiram Clawson]

Good Morning Morgaine:

You could try using the blat binary already built from:

http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat/

Your MACHTYPE of x86_64-pc-linux-gnu is not going to work due
to the - characters in the name.

It should simply be: x86_64
and it needs to be 'export' to get into your build. You should
see it on the compile lines as the binary is built.
That may help your build if the binary from hgdownload does not work.

--Hiram

[Cath Tyner]

Hi Morgaine! Thanks for writing to us with your question. 

To install blat on your Linux system, you can simply use the "wget" command to install the precompiled binary from our hgdownload server, like this:

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat

Once downloaded, you should change the permissions, to make the utility executable:

chmod +x blat

You can put blat in your "bin" directory if you have "added ~/bin to your path":http://stackoverflow.com/questions/10767738/how-do-i-add-bin-to-my-path,

or you can execute blat from whichever directory it is in by going to that directory and typing "dot forwardslash blat" like this:

,/blat

You can get the usage statement from blat by running it without parameters. Just type "blat" (or ./blat if needed) on your command line. The usage statement will look like this (only the first few lines are pasted below):

blat - Standalone BLAT v. 36x2 fast sequence search command line tool

usage:

   blat database query [-ooc=11.ooc] output.psl

where:

   database and query are each either a .fa, .nib or .2bit file,

      or a list of these files with one file name per line.

You can also see the full usage statement on the Blat User guide.

You can search our Public Support Forum for blat examples and answered questions (type "blat" into the search field or any related terms you would like to search for).

You can also do google searches for "ucsc blat" and find other resources, such as:

https://www.biostars.org/p/201904/

Or, too use your previous procedure, see this previously answered mailing list question, which explains that you need to patch the jkOwnLib/makefile:

Replace this:

ar rcus $(T) $(O)

with this:

libtool -static -o $(T) $(O)

Please respond to this list if you have further questions!

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

​Please send new and follow-up questions to one of our UCSC Genome Browser 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

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

  * Subscribe: Email genome-announce+subscribe@soe.ucsc.edu 
  * Unsubscribe: Email genome-announce+unsubscribe@soe.ucsc.edu

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

​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 discussion list" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.