Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

This page was last updated on Tuesday, 13-Aug-2019 09:07:39 CDT

Installation notes for blat version 34

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Prerequisites

None

Installation

  1. $ ver="34"
  2. $ cd /programinstallers/
  3. $ wget -N http://users.soe.ucsc.edu/~kent/src/blatSrc$ver.zip
  4. $ unzip blatSrc$ver.zip
  5. $ cd blatSrc
  6. $ mkdir -p ~/bin/x86_64
  7. $ make 'MACHTYPE = x86_64'
    ... 
    gcc -O  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DJK_WARN -Wall -Werror -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc  -o chainBlock.o -c chainBlock.c
chainBlock.c: In function ‘findBestPredecessors’:
chainBlock.c:290:16: error: variable ‘bestLeaf’ set but not used [-Werror=unused-but-set-variable]
 struct kdLeaf *bestLeaf = NULL;
                ^
cc1: all warnings being treated as errors
make[1]: *** [chainBlock.o] Error 1
make[1]: Leaving directory `/programinstallers/blatSrc/lib'
make: *** [all] Error 2
  8. This fix was not necessary for version 35 So make this change to the makefile include file
    $ nano inc/common.mk
    Line 17 change
    HG_WARN_ERR = -DJK_WARN -Wall -Werror
    to
    HG_WARN_ERR = -DJK_WARN -Wall
  9. $ make 'MACHTYPE = x86_64'
    ...
    gcc -O -o webBlat webBlat.o ../lib/x86_64/jkOwnLib.a ../lib/x86_64/jkweb.a -lm 
strip webBlat
make[1]: Leaving directory `/programinstallers/blatSrc/webBlat'
  10. Install
    $ cp -puv ~/bin/x86_64/* /usr/local/bin/
    ‘/home/dsenalik/bin/x86_64/blat’ -> ‘/usr/local/bin/blat’
‘/home/dsenalik/bin/x86_64/faToNib’ -> ‘/usr/local/bin/faToNib’
‘/home/dsenalik/bin/x86_64/faToTwoBit’ -> ‘/usr/local/bin/faToTwoBit’
‘/home/dsenalik/bin/x86_64/gfClient’ -> ‘/usr/local/bin/gfClient’
‘/home/dsenalik/bin/x86_64/gfServer’ -> ‘/usr/local/bin/gfServer’
‘/home/dsenalik/bin/x86_64/nibFrag’ -> ‘/usr/local/bin/nibFrag’
‘/home/dsenalik/bin/x86_64/pslPretty’ -> ‘/usr/local/bin/pslPretty’
‘/home/dsenalik/bin/x86_64/pslReps’ -> ‘/usr/local/bin/pslReps’
‘/home/dsenalik/bin/x86_64/pslSort’ -> ‘/usr/local/bin/pslSort’
‘/home/dsenalik/bin/x86_64/twoBitInfo’ -> ‘/usr/local/bin/twoBitInfo’
‘/home/dsenalik/bin/x86_64/twoBitToFa’ -> ‘/usr/local/bin/twoBitToFa’
  11. Cleanup
    $ rm ~/bin/x86_64 -rf
  12. $ rmdir ~/bin
  13. $ cd ..
  14. $ rm blatSrc -rf

In the future make /usr/local/bin/kent/ and put this there, adding to the default PATH in /etc/profile as usual
Also install chainNet.zip and liftOver.gz from https://hgwdev.gi.ucsc.edu/~kent/exe/linux/