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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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./configure checking samtools... failed #47

Closed winni-liu closed 4 years ago

winni-liu commented 6 years ago

I configure by this code ./configure --with-samtools=/psd/biosoft/samtools_suit/samtools-0.1.19/ --with-boost=/psd/biosoft/boost_1_60_0_b1/ but I get the error messages ：

...................... checking if samtools is wanted... yes checking sam.h usability... yes checking sam.h presence... yes checking for sam.h... yes 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

also, I have tested other way and configure: export LACHESIS_BOOST_DIR="/psd/biosoft/boost_1_60_0_b1/:$LACHESIS_BOOST_DIR" export LACHESIS_SAMTOOLS_DIR="/psd/biosoft/samtools_suit/samtools-0.1.19/:$LACHESIS_SAMTOOLS_DIR"

but it didn't work, Samtools is well installed and available。

wenjiexiaomeng commented 6 years ago

Hi, when i install this, it occurs the same error with u, have u figured out this ?

kfletcher88 commented 6 years ago

What does your samtools installation directory look like? I got this to work when all binaries, libraries and executables were in the top directory. This can be obtained with this command: git clone git://github.com/samtools/samtools.git

The install didn't work when they were in sub-directories (e.g. bin and lib).

Hope it helps!

fire-activate commented 2 years ago

I configure by this code ./configure --with-samtools=/psd/biosoft/samtools_suit/samtools-0.1.19/ --with-boost=/psd/biosoft/boost_1_60_0_b1/ but I get the error messages ：

...................... checking if samtools is wanted... yes checking sam.h usability... yes checking sam.h presence... yes checking for sam.h... yes 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

also, I have tested other way and configure: export LACHESIS_BOOST_DIR="/psd/biosoft/boost_1_60_0_b1/:$LACHESIS_BOOST_DIR" export LACHESIS_SAMTOOLS_DIR="/psd/biosoft/samtools_suit/samtools-0.1.19/:$LACHESIS_SAMTOOLS_DIR"