Question: error on installing samtools on linux cluster
0
gravatar for bsmith030465
2.1 years ago by
bsmith030465140
United States
bsmith030465140 wrote:

Hi,

I was trying to install samtools in my account on a linux cluster (x86_64 GNU/Linux). I downloaded the samtools tar.bz2 from http://www.htslib.org/download/ . After unzipping all the files, I cd into the directory and run 'make install'. However, I get an error:

[bsm@submit-3 samtools-1.4]$ make install cd htslib-1.4 && make lib-static make[1]: Entering directory /home/bsm/software/samtools-1.4/htslib-1.4' gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c cram/cram_io.c:60:18: error: lzma.h: No such file or directory cram/cram_io.c: In function ‘lzma_mem_deflate’: cram/cram_io.c:865: warning: implicit declaration of function ‘lzma_stream_buffer_bound’ cram/cram_io.c:871: error: ‘LZMA_OK’ undeclared (first use in this function) cram/cram_io.c:871: error: (Each undeclared identifier is reported only once cram/cram_io.c:871: error: for each function it appears in.) cram/cram_io.c:871: warning: implicit declaration of function ‘lzma_easy_buffer_encode’ cram/cram_io.c:871: error: ‘LZMA_CHECK_CRC32’ undeclared (first use in this function) cram/cram_io.c: In function ‘lzma_mem_inflate’: cram/cram_io.c:881: error: ‘lzma_stream’ undeclared (first use in this function) cram/cram_io.c:881: error: expected ‘;’ before ‘strm’ cram/cram_io.c:887: error: ‘LZMA_OK’ undeclared (first use in this function) cram/cram_io.c:887: warning: implicit declaration of function ‘lzma_stream_decoder’ cram/cram_io.c:887: error: ‘strm’ undeclared (first use in this function) cram/cram_io.c:887: warning: implicit declaration of function ‘lzma_easy_decoder_memusage’ cram/cram_io.c:902: warning: implicit declaration of function ‘lzma_code’ cram/cram_io.c:902: error: ‘LZMA_RUN’ undeclared (first use in this function) cram/cram_io.c:903: error: ‘LZMA_STREAM_END’ undeclared (first use in this function) cram/cram_io.c:915: error: ‘LZMA_FINISH’ undeclared (first use in this function) cram/cram_io.c:924: warning: implicit declaration of function ‘lzma_end’ make[1]: *** [cram/cram_io.o] Error 1 make[1]: Leaving directory/home/bsm/software/samtools-1.4/htslib-1.4' make: * [htslib-1.4/libhts.a] Error 2

what do I need to do?

thanks!

--sorry for the bad formatting! I don't know how I should correct it :(

samtools • 3.9k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by bsmith030465140
1

In this thread scroll down and look up an answer that mentions issue #570. See if that fixes this issue.

ADD REPLYlink written 2.1 years ago by genomax67k
1
gravatar for h.mon
2.1 years ago by
h.mon25k
Brazil
h.mon25k wrote:

You are missing the lzma headers, and you need to install the development package for lzma. On Debian and Ubuntu, it is called liblzma-devel. You probably have to ask your sys admin to install it for you.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by h.mon25k
2

The dependency can be turned off as mentioned in this thread.

ADD REPLYlink written 2.1 years ago by genomax67k

Thanks, that worked!

ADD REPLYlink written 2.1 years ago by bsmith030465140

for me this should be the correct answer thanks !

ADD REPLYlink written 11 months ago by pratt0
0
gravatar for Praneet Chaturvedi
2.1 years ago by
Cincinnati Children's Hospital and Medical Center
Praneet Chaturvedi110 wrote:

sudo apt-get install build-essential sudo apt-get install samtools

ADD COMMENTlink written 2.1 years ago by Praneet Chaturvedi110
0
gravatar for bsmith030465
2.1 years ago by
bsmith030465140
United States
bsmith030465140 wrote:

Thanks all! The thread suggested by genomax2 worked!

ADD COMMENTlink written 2.1 years ago by bsmith030465140
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