Trouble Installing Blat Executables
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11.1 years ago
agatorano ▴ 50

I am getting this error when I run the make command on an executable.

gcc -O -g -Wall -Wno-unused-variable -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DUSE_SSL -DCOLOR32 -Wall -Wno-unused-variable -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o fixCr.o -c fixCr.c gcc -O -g -Wall -Wno-unused-variable -o /Users/andregatorano/bin//fixCr fixCr.o ../../lib//jkweb.a -pthread -lssl -lcrypto -lpng i686-apple-darwin11-llvm-gcc-4.2: ../../lib//jkweb.a: No such file or directory make: * [fixCr] Error 1

Is there an obvious mistake?

blat • 9.3k views
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Just at the same time... Looks like you are missing the jkweb library.

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Do you know where that may be?

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What have your tried? I use Blat quite frequently but I can't tell what is going on here and have never had a problem installing it. Did you entirely download the newest version?

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3
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11.1 years ago

This post should solve your problem (about jkweb library), compiling BLAT, 'No rule to make target '../lib//jkweb.a', needed by `blat'. Stop.' referred here Adventures with installing blat on Mac OS X

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Thank you my machtype was empty. I have it set in my .bashrc file but it seems to only be in my environmental variables when it I export from the command line. Do I need to do this everytime?

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I don't think so, once you sourced the .bashrc, it should auto load with every boot!!

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7.6 years ago

3.6 years later and here I am - Sukhdeep's link at https://lists.soe.ucsc.edu is now dead, this solved compiling BLAT for me:

make MACHTYPE=$MACHTYPE
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7.6 years ago
brianlee • 0

The UCSC mail archives moved from https://lists.soe.ucsc.edu to a google group: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!forum/genome

You can search for the referenced subject line "No rule to make target ../lib//jkweb.a', needed byblat'. Stop." to find the email: https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/%22No$20rule$20to$20make$20target$20%60..$2Flib$2F$2Fjkweb.a$27$2C$20needed$20by$20%60blat$27.$20Stop.%22

If you only have the older links, it requires some more searching to find. For example, with the link like https://lists.soe.ucsc.edu/pipermail/genome/2009-November/020471.html one trick is to try the way back machine http://archive.org/web/

Another approach is by using the date (2009 Nov) you can filter the google group to with the filter for those dates (Posted after X Posted before Y subject).

after:2009/11/01 AND before:2009/12/01 blat

https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!topicsearchin/genome/after$3A2009$2F11$2F01$20AND$20before$3A2009$2F12$2F01$20blat


Please know UCSC supports several lists where users can email questions:

-For posting general non-mirror and non-confidential questions: * Post to the Public Help Forum: Email genome@soe.ucsc.edu​ or search the Public Archives: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome

-For posting mirror-related questions: ​ * Post to the Mirror Help Forum: Email genome-mirror@soe.ucsc.edu or search the Mirror Archives​: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror

-For posting questions with information that is private/confidential: ​ * Email genome-www@soe.ucsc.edu

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