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8.3 years ago
2013302630028
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10
I want to install a localized UCSC Genome browser in my server. I try to use the Oliver's method to install it, and this is the [link][1]. When I install fixCr in $kent/src/utils/fixCr I get some undefined reference errors. My command is in the end. Thank you for your help~
sqreb@sqreb-Vostro-1450:~/genome/kent/src/utils/fixCr$ make gcc -O -g -o /home/sqreb/bin/x86_64/fixCr fixCr.o ../../lib/x86_64/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lstdc++ -lrt -lm ../../htslib/libhts.a -pthread -L/lib -lssl -lcrypto -lpng12 -lm ../../htslib/libhts.a(hts.o): In function `decompress_peek': /home/sqreb/genome/kent/src/htslib/hts.c:142: undefined reference to `inflateInit2_' /home/sqreb/genome/kent/src/htslib/hts.c:145: undefined reference to `inflate' /home/sqreb/genome/kent/src/htslib/hts.c:148: undefined reference to `inflateEnd' ../../htslib/libhts.a(cram_io.o): In function `itf8_decode_crc': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:195: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:201: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:208: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:216: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:225: undefined reference to `crc32' ../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:537: more undefined references to `crc32' follow ../../htslib/libhts.a(cram_io.o): In function `zlib_mem_inflate': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:718: undefined reference to `inflateInit2_' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:731: undefined reference to `inflate' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:751: undefined reference to `inflateEnd' ../../htslib/libhts.a(cram_io.o): In function `zlib_mem_deflate': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:782: undefined reference to `deflateInit2_' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:796: undefined reference to `deflate' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:803: undefined reference to `deflate' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:808: undefined reference to `deflateEnd' ../../htslib/libhts.a(cram_io.o): In function `cram_read_block': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:946: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:948: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:980: undefined reference to `crc32' ../../htslib/libhts.a(cram_io.o): In function `cram_write_block': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1049: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1052: undefined reference to `crc32' ../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1054: more undefined references to `crc32' follow ../../htslib/libhts.a(zfio.o): In function `zfgets': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:69: undefined reference to `gzgets' ../../htslib/libhts.a(zfio.o): In function `zfputs': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:80: undefined reference to `gzputs' ../../htslib/libhts.a(zfio.o): In function `zfpeek': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:95: undefined reference to `gzgetc' /home/sqreb/genome/kent/src/htslib/cram/zfio.c:97: undefined reference to `gzungetc' ../../htslib/libhts.a(zfio.o): In function `zfeof': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:105: undefined reference to `gzeof' ../../htslib/libhts.a(zfio.o): In function `zfopen': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:165: undefined reference to `gzopen' /home/sqreb/genome/kent/src/htslib/cram/zfio.c:169: undefined reference to `gzopen' ../../htslib/libhts.a(zfio.o): In function `zfclose': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:180: undefined reference to `gzclose' ../../htslib/libhts.a(bgzf.o): In function `bgzf_write_init': /home/sqreb/genome/kent/src/htslib/bgzf.c:166: undefined reference to `deflateInit2_' ../../htslib/libhts.a(bgzf.o): In function `bgzf_open': /home/sqreb/genome/kent/src/htslib/bgzf.c:174: undefined reference to `compressBound' ../../htslib/libhts.a(bgzf.o): In function `bgzf_dopen': /home/sqreb/genome/kent/src/htslib/bgzf.c:196: undefined reference to `compressBound' ../../htslib/libhts.a(bgzf.o): In function `bgzf_hopen': /home/sqreb/genome/kent/src/htslib/bgzf.c:218: undefined reference to `compressBound' ../../htslib/libhts.a(bgzf.o): In function `bgzf_compress': /home/sqreb/genome/kent/src/htslib/bgzf.c:244: undefined reference to `deflateInit2_' /home/sqreb/genome/kent/src/htslib/bgzf.c:245: undefined reference to `deflate' /home/sqreb/genome/kent/src/htslib/bgzf.c:246: undefined reference to `deflateEnd' /home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32' ../../htslib/libhts.a(bgzf.o): In function `bgzf_gzip_compress': /home/sqreb/genome/kent/src/htslib/bgzf.c:267: undefined reference to `deflate' ../../htslib/libhts.a(bgzf.o): In function `inflate_block': /home/sqreb/genome/kent/src/htslib/bgzf.c:302: undefined reference to `inflateInit2_' /home/sqreb/genome/kent/src/htslib/bgzf.c:306: undefined reference to `inflate' /home/sqreb/genome/kent/src/htslib/bgzf.c:307: undefined reference to `inflateEnd' /home/sqreb/genome/kent/src/htslib/bgzf.c:311: undefined reference to `inflateEnd' ../../htslib/libhts.a(bgzf.o): In function `inflate_gzip_block': /home/sqreb/genome/kent/src/htslib/bgzf.c:335: undefined reference to `inflate' ../../htslib/libhts.a(bgzf.o): In function `bgzf_read_block': /home/sqreb/genome/kent/src/htslib/bgzf.c:505: undefined reference to `inflateInit2_' ../../htslib/libhts.a(bgzf.o): In function `bgzf_close': /home/sqreb/genome/kent/src/htslib/bgzf.c:816: undefined reference to `inflateEnd' /home/sqreb/genome/kent/src/htslib/bgzf.c:817: undefined reference to `deflateEnd' collect2: error: ld returned 1 exit status ../../inc/userApp.mk:31: recipe for target '/home/sqreb/bin/x86_64/fixCr' failed make: *** [/home/sqreb/bin/x86_64/fixCr] Error 1
--This is my command.-- Set MACHTYPE
sqreb@sqreb-Vostro-1450:~$ uname -a
Linux sqreb-Vostro-1450 4.4.0-34-generic #53-Ubuntu SMP Wed Jul 27 16:06:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
sqreb@sqreb-Vostro-1450:~$ MACHTYPE=x86_64
sqreb@sqreb-Vostro-1450:~$ export MACHTYPE
sqreb@sqreb-Vostro-1450:~$ mkdir -p ~/bin/${MACHTYPE}
Download USCS source codes
sqreb@sqreb-Vostro-1450:~$ cd genome/ sqreb@sqreb-Vostro-1450:~/genome$ git clone git://genome-source.cse.ucsc.edu/kent.git Cloning into 'kent'... Checking connectivity... done. sqreb@sqreb-Vostro-1450:~/genome$ git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix Cloning into 'samtabix'... Checking connectivity... done.
MySQL option
sqreb@sqreb-Vostro-1450:~/genome$ mysql_config --libs -L/usr/local/mysql/lib -lmysqlclient -lpthread -lm -lrt -ldl sqreb@sqreb-Vostro-1450:~/genome$ mysql_config --include -I/usr/local/mysql/include sqreb@sqreb-Vostro-1450:~/genome$ MYSQLINC=/usr/local/mysql sqreb@sqreb-Vostro-1450:~/genome$ MYSQLLIBS="/usr/local/mysql/lib/libmysqlclient.a -lz" sqreb@sqreb-Vostro-1450:~/genome$ export MYSQLINC MYSQLLIBS
SSL and SAM/BAM and tabix (for VCF) option
Add those command in common.mk USE_SSL=1 USE_SAMTABIX=1 SAMTABIXDIR=/home/sqreb/genome/samtabix
Install UCSC Genome browser
sqreb@sqreb-Vostro-1450:~/genome$ cd kent/src sqreb@sqreb-Vostro-1450:~/genome/kent/src$ make libs cd lib && make make[1]: Entering directory '/home/sqreb/genome/kent/src/lib' ... make[1]: Leaving directory '/home/sqreb/genome/kent/src/hg/lib' sqreb@sqreb-Vostro-1450:~/genome/kent/src$ cd utils/fixCr/ sqreb@sqreb-Vostro-1450:~/genome/kent/src/utils/fixCr$ make gcc -O -g -o /home/sqreb/bin/x86_64/fixCr fixCr.o ../../lib/x86_64/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lstdc++ -lrt -lm ../../htslib/libhts.a -pthread -L/lib -lssl -lcrypto -lpng12 -lm ../../htslib/libhts.a(hts.o): In function `decompress_peek': /home/sqreb/genome/kent/src/htslib/hts.c:142: undefined reference to `inflateInit2_' /home/sqreb/genome/kent/src/htslib/hts.c:145: undefined reference to `inflate' /home/sqreb/genome/kent/src/htslib/hts.c:148: undefined reference to `inflateEnd' ../../htslib/libhts.a(cram_io.o): In function `itf8_decode_crc': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:195: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:201: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:208: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:216: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:225: undefined reference to `crc32' ../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:537: more undefined references to `crc32' follow ../../htslib/libhts.a(cram_io.o): In function `zlib_mem_inflate': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:718: undefined reference to `inflateInit2_' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:731: undefined reference to `inflate' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:751: undefined reference to `inflateEnd' ../../htslib/libhts.a(cram_io.o): In function `zlib_mem_deflate': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:782: undefined reference to `deflateInit2_' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:796: undefined reference to `deflate' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:803: undefined reference to `deflate' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:808: undefined reference to `deflateEnd' ../../htslib/libhts.a(cram_io.o): In function `cram_read_block': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:946: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:948: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:980: undefined reference to `crc32' ../../htslib/libhts.a(cram_io.o): In function `cram_write_block': /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1049: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1052: undefined reference to `crc32' ../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1054: more undefined references to `crc32' follow ../../htslib/libhts.a(zfio.o): In function `zfgets': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:69: undefined reference to `gzgets' ../../htslib/libhts.a(zfio.o): In function `zfputs': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:80: undefined reference to `gzputs' ../../htslib/libhts.a(zfio.o): In function `zfpeek': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:95: undefined reference to `gzgetc' /home/sqreb/genome/kent/src/htslib/cram/zfio.c:97: undefined reference to `gzungetc' ../../htslib/libhts.a(zfio.o): In function `zfeof': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:105: undefined reference to `gzeof' ../../htslib/libhts.a(zfio.o): In function `zfopen': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:165: undefined reference to `gzopen' /home/sqreb/genome/kent/src/htslib/cram/zfio.c:169: undefined reference to `gzopen' ../../htslib/libhts.a(zfio.o): In function `zfclose': /home/sqreb/genome/kent/src/htslib/cram/zfio.c:180: undefined reference to `gzclose' ../../htslib/libhts.a(bgzf.o): In function `bgzf_write_init': /home/sqreb/genome/kent/src/htslib/bgzf.c:166: undefined reference to `deflateInit2_' ../../htslib/libhts.a(bgzf.o): In function `bgzf_open': /home/sqreb/genome/kent/src/htslib/bgzf.c:174: undefined reference to `compressBound' ../../htslib/libhts.a(bgzf.o): In function `bgzf_dopen': /home/sqreb/genome/kent/src/htslib/bgzf.c:196: undefined reference to `compressBound' ../../htslib/libhts.a(bgzf.o): In function `bgzf_hopen': /home/sqreb/genome/kent/src/htslib/bgzf.c:218: undefined reference to `compressBound' ../../htslib/libhts.a(bgzf.o): In function `bgzf_compress': /home/sqreb/genome/kent/src/htslib/bgzf.c:244: undefined reference to `deflateInit2_' /home/sqreb/genome/kent/src/htslib/bgzf.c:245: undefined reference to `deflate' /home/sqreb/genome/kent/src/htslib/bgzf.c:246: undefined reference to `deflateEnd' /home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32' /home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32' ../../htslib/libhts.a(bgzf.o): In function `bgzf_gzip_compress': /home/sqreb/genome/kent/src/htslib/bgzf.c:267: undefined reference to `deflate' ../../htslib/libhts.a(bgzf.o): In function `inflate_block': /home/sqreb/genome/kent/src/htslib/bgzf.c:302: undefined reference to `inflateInit2_' /home/sqreb/genome/kent/src/htslib/bgzf.c:306: undefined reference to `inflate' /home/sqreb/genome/kent/src/htslib/bgzf.c:307: undefined reference to `inflateEnd' /home/sqreb/genome/kent/src/htslib/bgzf.c:311: undefined reference to `inflateEnd' ../../htslib/libhts.a(bgzf.o): In function `inflate_gzip_block': /home/sqreb/genome/kent/src/htslib/bgzf.c:335: undefined reference to `inflate' ../../htslib/libhts.a(bgzf.o): In function `bgzf_read_block': /home/sqreb/genome/kent/src/htslib/bgzf.c:505: undefined reference to `inflateInit2_' ../../htslib/libhts.a(bgzf.o): In function `bgzf_close': /home/sqreb/genome/kent/src/htslib/bgzf.c:816: undefined reference to `inflateEnd' /home/sqreb/genome/kent/src/htslib/bgzf.c:817: undefined reference to `deflateEnd' collect2: error: ld returned 1 exit status ../../inc/userApp.mk:31: recipe for target '/home/sqreb/bin/x86_64/fixCr' failed make: *** [/home/sqreb/bin/x86_64/fixCr] Error 1
Have you solved this issue? I have a similar problem.