Comments (15)
You need to install the google sparse hash library
http://code.google.com/p/sparsehash/
I'll ship it with future releases... it's small.
Original comment by [email protected]
on 9 Jul 2012 at 1:42
from ea-utils.
Let me know if this works for you.
Original comment by [email protected]
on 9 Jul 2012 at 1:42
- Added labels: Type-Other
- Removed labels: Type-Defect
from ea-utils.
Hi,
I wanted to know that I installed the google sparse hash library ,LOCALLY on
server ./configure --prefix=/home/figo/local
But how i can configure the ea-utils.1.1.2, since it doesn't contain the
.configure file, so how I can configure the ea-utils make file to go to my
local installation directory to look for the google sparse has library.(I
really don't know do i need to change some thing in the make file for this)
Original comment by [email protected]
on 24 Jul 2012 at 8:53
from ea-utils.
You can soft link google->directory where it's installed (that's how i like to
do things)
or you can specify an include path for g++
Original comment by [email protected]
on 25 Jul 2012 at 6:01
from ea-utils.
Thanks for the tools.
I have the same error while installing. Simply set the include path in you
~/.bashrc like this:
export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:$HOME/include
export C_INCLUDE_PATH=$C_INCLUDE_PATH:$HOME/include
this can solve the problem.
Original comment by [email protected]
on 27 Jul 2012 at 7:22
from ea-utils.
Soft linking to the compiled sparsehash and editing Makefile fixed the problem
for me...
Hope this helps..
Inside the extracted directory...
.
.
sparsehash -> sparsehash-2.0.2
.
.
diff for changed and original Makefile
>>>>>>>>>>>>>>>>>>>>
43c43
< $(CC) $(CFLAGS) -I./sparsehash/include fastq-lib.cpp -o $@ $<
---
> $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
46c46
< $(CC) $(CFLAGS) -I./sparsehash/include fastq-lib.cpp -o $@ $<
---
> $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
50c50
< $(CC) $(CFLAGS) -I./sparsehash/include fastq-lib.cpp -lbamtools -o $@ $<
---
> $(CC) $(CFLAGS) -I. fastq-lib.cpp -lbamtools -o $@ $<
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
Original comment by [email protected]
on 13 Aug 2012 at 4:42
from ea-utils.
[deleted comment]
from ea-utils.
Hi all, I seem to having a similar issue on install, output:
g++ -O3 -I. fastq-lib.cpp -o fastq-mcf fastq-mcf.c
g++ -O3 -I. fastq-lib.cpp -o fastq-multx fastq-multx.c
fastq-multx.c: In function ‘int main(int, char**)’:
fastq-multx.c:275:29: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:276:29: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:493:25: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:494:25: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:531:25: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
g++ -O3 -I. fastq-lib.cpp -o fastq-join fastq-join.c
g++ -O3 -I. fastq-lib.cpp -o fastq-stats fastq-stats.cpp
In file included from fastq-stats.cpp:34:0:
./google/sparse_hash_map:34:38: fatal error: sparsehash/sparse_hash_map: No
such file or directory
compilation terminated.
Seems strange because, despite the last line, the sparse_hash_map seems to be
there! So I'm assuming the sparsehash pack is now included in the newest
release, as promised (?)
This is on Ubuntu 12.04.
Original comment by [email protected]
on 19 Sep 2012 at 3:57
from ea-utils.
So you essentially added "-I./sparsehash/include" ... ? (I'm also running
12.04 LTS)
I uploaded this version
ea-utils.1.1.2-469.tar.gz
It should have everything needed to compile.
Original comment by [email protected]
on 19 Sep 2012 at 4:24
from ea-utils.
Thanks for adding the new version and your quick reply. However, I'm still
getting this error from running make:
g++ -O3 -I. fastq-lib.cpp -o fastq-mcf fastq-mcf.c
g++ -O3 -I. fastq-lib.cpp -o fastq-multx fastq-multx.c
fastq-multx.c: In function ‘int main(int, char**)’:
fastq-multx.c:275:29: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:276:29: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:493:25: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:494:25: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
fastq-multx.c:531:25: warning: ignoring return value of ‘__ssize_t
getline(char**, size_t*, FILE*)’, declared with attribute warn_unused_result
[-Wunused-result]
g++ -O3 -I. fastq-lib.cpp -o fastq-join fastq-join.c
g++ -O3 -I. fastq-lib.cpp -o fastq-stats fastq-stats.cpp
g++ -O3 -I. fastq-lib.cpp -o fastq-clipper fastq-clipper.c
g++ -O3 -I. fastq-lib.cpp -lbamtools -o sam-stats sam-stats.cpp
sam-stats.cpp:40:27: fatal error: api/BamReader.h: No such file or directory
compilation terminated.
make: *** [sam-stats] Error 1
Original comment by [email protected]
on 19 Sep 2012 at 4:37
from ea-utils.
Generally, that's not really an issue... unless you want to build sam-stats.
If you do, please install this first:
https://github.com/pezmaster31/bamtools/wiki/Building-and-installing
I should probably detect to see if it's installed and make it conditional ...
ie just warn you that bamtools isn't installed.
I think bundling all of bamtools would be a bit much, but maybe not.
Original comment by [email protected]
on 19 Sep 2012 at 4:41
from ea-utils.
[deleted comment]
from ea-utils.
I thin all the tools have built (fastq-join, etc. should be in the directory).
To avoid errors, you can either a) remove the reference to sam-stats in the
BIN variable or b) install bamtools.
Original comment by [email protected]
on 19 Sep 2012 at 5:43
from ea-utils.
Thanks for the comment. Brain fart: I was removing the directory without
checking to make sure the tools where installed correctly. They were, so I
removed comment 12.
Original comment by [email protected]
on 19 Sep 2012 at 10:12
from ea-utils.
i'm going to ditch bamtools in the next release, which will aso include a lot
of rna-seq specific stuff, and support for walking through bwa's
mutltiple-alignment XA tags
closing this issue as "resolved" for now
Original comment by [email protected]
on 20 Sep 2012 at 6:13
- Changed state: Fixed
from ea-utils.
Related Issues (20)
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- fastq-mcf not working correctly on ubuntu 14.04 HOT 9
- error message: "fastq-mcf has stopped working" HOT 4
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