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ucscGenomeBrowser / kent

UCSC Genome Browser source tree. Stable branch: "beta".
http://genome.ucsc.edu/
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Issue with fixCr #24

Closed ashlingcha closed 4 years ago

ashlingcha commented 4 years ago

Hi there, when I try to make fixCr, fixCr.o is made but not gotCr.c this is the output: /bin/sh: mysql_config: command not found /bin/sh: mysql_config: command not found gcc -O -g -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/usr/include/libpng16 -o fixCr.o -c fixCr.c gcc -O -g -o /home/ashling_charles/bin/x86_64/fixCr fixCr.o ../../lib/x86_64/jkweb.a "-L/usr/lib64 -lmysqlclient" -lstdc++ -lrt -lpthread -lssl -lcrypto ../../htslib/libhts.a -L/usr/lib64 -lpng16 -lm -lz true /home/ashling_charles/bin/x86_64/fixCr

I know without this hal wont work. Thanks in advance.

ashlingcha commented 4 years ago

It may have to do with this part of the instructions: 'rehash' if necessary so your shell can find the fixcr program in ~/bin/$(MACHTYPE). May be a silly question but what is $(MACHTYPE) in this context?

maximilianh commented 4 years ago

MACHTYPE is explained in the main README file.

Instead of building the tools yourself, don't you prefer to download them precompiled, from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ ?

On Sun, Jan 12, 2020 at 10:19 PM ashlingcha notifications@github.com wrote:

It may have to do with this part of the instructions: 'rehash' if necessary so your shell can find the fixcr program in ~/bin/$(MACHTYPE). May be a silly question but what is $(MACHTYPE) in this context?

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ashlingcha commented 4 years ago

The link you sent me looks like they're for the lastz alignment tools, whereas I'm trying to compile the haltools which requires kent. (https://github.com/ComparativeGenomicsToolkit/hal) I don't mind getting them precompiled I just need to get the tools. thanks

maximilianh commented 4 years ago

Oh! Don’t the haltools mention how to build the kent tools ? There is no need to set machtype anymore. What does the haltools docs say what you should do?

On Mon 13 Jan 2020 at 08:40, ashlingcha notifications@github.com wrote:

The link you sent me looks like they're for the lastz alignment tools, whereas I'm trying to compile the haltools which requires kent. ( https://github.com/ComparativeGenomicsToolkit/hal) I don't mind getting them precompiled I just need to get the tools. thanks

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ashlingcha commented 4 years ago

haltools only mentions that I should be pointing to the kentsrc tree - I had it working before but for some reason I had to reinstall kent and ever since I've had troubles compiling it These are the instructions:


cd $MYGROUP
git clone https://github.com/ucscGenomeBrowser/kent.git
cd kent (compile the packages as required)

cd $MYGROUP
git clone https://github.com/ComparativeGenomicsToolkit/hal.git

export  ENABLE_UDC=1
export KENTSRC=$MYGROUP/kent/src (i've cloned kent in my group directory)
git clone https://github.com/benedictpaten/sonLib.git
pushd sonLib && make && popd

cd hal
make
maximilianh commented 4 years ago

@glennhickey any suggestions ?

On Tue 14 Jan 2020 at 07:40, ashlingcha notifications@github.com wrote:

I tried to make a directory called kent and put all the prebuilt tools in there via http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ but that didn't work

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maximilianh commented 4 years ago

Yes you’ll need to build the Kent source tree . Glenn will have an idea why or which parts. Does a simple “cd kent/src; make -j8” not work for you?

On Tue 14 Jan 2020 at 14:23, Maximilian Haeussler maximilianh@gmail.com wrote:

@glennhickey any suggestions ?

On Tue 14 Jan 2020 at 07:40, ashlingcha notifications@github.com wrote:

I tried to make a directory called kent and put all the prebuilt tools in there via http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ but that didn't work

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glennhickey commented 4 years ago

HAL's build only depends on the Kent source tree when the ENABLE_UDC environment variable is set..

Unless you are building HAL in order to link it to a custom build of the UCSC genome browser which you want to use as a back-end for visualizing snake tracks, then there is no reason a I can think of to build it this way. This is touched on a bit in HAL's README.

@ashlingcha Are you trying to build the genome browser along with hal? Where do the instructions which you posted that include export ENABLE_UDC=1 come from?

ashlingcha commented 4 years ago

I'm trying to just build hal. Those instructions were given to me by the pawsey helpdesk, and have worked before but I can't get it to run this time.

maximilianh commented 4 years ago

You don't need the UCSC kent tree to build HAL.

ashlingcha commented 4 years ago

Thanks, I've gotten hal to work without kent now - unsure why I was advised to install it this way. Thanks for your help.