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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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configuration ERROR with samtools #59

Open WTarabidopsis opened 5 years ago

WTarabidopsis commented 5 years ago

Hi, When I was configuring LACHESIS, an ERROR about samtools always came up. The samtools have already been installed and I gave it the DIR. However, it could not recognize the samtools. The command for configuration is 

./configure --with-samtools=/lustre/home/jiayuxin/1-softwares/samtools/

Part of the ERROR messages are as follows:

checking if samtools is wanted... yes
checking sam.h usability... no
checking sam.h presence... no
checking for sam.h... no
checking for sam_open in -lbam... no
checking samtools... failed
configure: error: either specify a valid samtools installation with --with-samtools=DIR or disable samtools usage with --without-samtools

Even I disabled the use of samtools like this: ./configure --without-samtools It also ran ERROR:

checking if samtools is wanted... no
checking sam.h usability... no
checking sam.h presence... no
checking for sam.h... no
checking for sam_open in -lbam... no
checking samtools... failed
configure: error: either specify a valid samtools installation with --with-samtools=DIR or disable samtools usage with --without-samtools

Furthermore, I also tried to put the source files of samtools and the built file into the same directory, but it didn't help.

Could anyone help me with this problem? Thanks in advance!

wuxiaopei0509 commented 5 years ago

Hi,dear Have your problems been resolved? I have the same problem

WTarabidopsis commented 5 years ago

Hi, I found that the LACHESIS required an old version of samtools and the installation package was included in LACHESIS package. After you unpack LACHESIS, it should be located at ./LACHESIS/src/include Good luck.

anupullanhi commented 3 years ago

Hi, I got the same error for samtools while running configure as shown below:

Command used - ./configure --with-samtools=./src/include/samtools-legacy_0.1.19_debian

Error: checking for sam_open in -lbam... no checking samtools... failed configure: error: either specify a valid samtools installation with --with-samtools=DIR or disable samtools usage with --without-samtools

I tried the export commands as well but it didn't work. Any help in resolving this issue is appreciated.

Thank you