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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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bam/sam.h #54

Open simonkidd opened 5 years ago

simonkidd commented 5 years ago

Hi

After a successful ./configure I run make I get an fatal error that reads:

make[1]: Entering directory `.../shendurelab-LACHESIS-2e27abb/src/include/gtools'
g++ -c SAMStepper.cc -Wall -ansi -pedantic -g -O3 -std=c++11 
In file included from SAMStepper.cc:18:0:
**SAMStepper.h:65:21: fatal error: bam/sam.h: No such file or directory**
 **#include <bam/sam.h>**
                     ^
compilation terminated.
make[1]: *** [SAMStepper.o] Error 1

I tried to get around the issue by creating a symbolic link back into samtools to where sam.h is within 'src/include/gtools/' (creating the bam folder 'src/include/gtools/bam/') but it still fails to read the file.

Any help would be really appreciated.

Thanks, Simon

pkubgmlixs commented 5 years ago

Hi, I got the same fatal error, too. And have you solved this error?

simonkidd commented 5 years ago

Sorry pkubgmlixs, I haven't had any responses andhaven't revisited it myself but will soon and post any update should I have any.

Thanks.

GitHub-Lujianjun commented 5 years ago

Hi guys： While this error appeared，means that your need to update gcc and g++. BTW, gcc-4.8.2 is necessary. Good luck! JJLu

WTarabidopsis commented 5 years ago

Hi guys： While this error appeared，means that your need to update gcc and g++. BTW, gcc-4.8.2 is necessary. Good luck! JJLu

Hi JJ, I also encountered the same problem with gcc version 4.8.5, any other solutions? Thanks!

mehmetdayi commented 4 years ago

Hi Did you solve it? I am having the same issue.

mehmetdayi commented 4 years ago

I solved and am adding solution here in case someone alse may need.

First you need to edit SAMStepper.h and SAMStepper.cc files in /src/include/gtools directory by adding the directory after -I flag and a bam.h file after #include line.

For instance (SAMStepper.h file editing);

// To compile using this, you must include -I /home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian

include "/home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian/sam.h"

You should do the same editing for SAMStepper.cc.

Then you can run make and later make install.

RanSenn commented 2 years ago

I solved and am adding solution here in case someone alse may need.

First you need to edit SAMStepper.h and SAMStepper.cc files in /src/include/gtools directory by adding the directory after -I flag and a bam.h file after #include line.

For instance (SAMStepper.h file editing);

// To compile using this, you must include -I /home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian #include "/home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian/sam.h"

You should do the same editing for SAMStepper.cc.

Then you can run make and later make install.

It works！Thank You Very Much！