Comments (13)
OK, I make a mingw port. Not too many changes were needed. You'll need to
get release 621.
Original comment by [email protected]
on 3 Jun 2013 at 1:16
from ea-utils.
(let me know if this works so i can close the ticket)
Original comment by [email protected]
on 3 Jun 2013 at 5:50
from ea-utils.
Sorry I am a lit bit confused how do I get the 621 . In your repository all the
Makefile, fastaq-lib.h, fastaq-lib.cpp & the sparseconfig.h are the modified
files that I need.
After some fooling around realised can't copy paste or wget them need them
through svn but not sure what to do. I did a svn checkout for all these 4files
and in the modifications it shows modified version 621 for these 4 files but
when I ran the "CC=g++ PREFIX=/usr/local make install" it is still giving me
error and I guess the same error as earlier
Original comment by [email protected]
on 4 Jun 2013 at 6:03
Attachments:
from ea-utils.
the big issue is that the windows socket library needs to be linked in. The
Makefile checks to see if you're on Windows by looking at the $OS variable and
then changing the linking variables (I am trying to avoid dealing with
"configure" for some reason). Also, the other code now checks for windows. I
successfully compiled all but "varcall" on mingw using windows 7.
when you ran svn checkout... did you compile FROM the checked-out directory...
or did you move things around first? try just "checkout ... make"
Original comment by [email protected]
on 4 Jun 2013 at 6:08
from ea-utils.
i could just upload the windows binaries.
Original comment by [email protected]
on 4 Jun 2013 at 6:09
from ea-utils.
I am unable to figure out what I am doing wrong. so I have my
ea-utilis.1.1.2-537 folder with all my files in there. I have downloaded
svntortoise.
I right click and go to svn checkout and it opens a new window .in the new
window in url "http://ea-utils.googlecode.com/svn/trunk/clipper/Makefile" in
the checkout directory "C:\Users\ea-utilis.1.1.2-537" checkout depth-fully
recursive, and selected head revision.
This shows the makefile with an red ! on the Makefile . I opened the diff file
and it shows working base revision 621 (the script file with the modified
codes) and the working copy with "ID-520....."(the older copy).
Please let me know if I am doing something wrong....
Original comment by [email protected]
on 6 Jun 2013 at 6:28
from ea-utils.
1. Did you try the precompiled executables? I uploaded them.... not sure if
you need libs to use them.
2. I don't know tortise, I just paste the command line Google gives you to
checkout.
3. The Makefile should have this in it:
ifeq ($(OS),Windows_NT)
$(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@
else
$(CC) $(CFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@
endif
Original comment by [email protected]
on 6 Jun 2013 at 6:35
from ea-utils.
where are the precompiled executables....I just saw the svn directory with the
4 modified files in version 621.
this time in my ea-utils folder I deleted these 4 files and did the checkout
for all these 4 files. I checked the makefile and it has the above lines in it.
I ran the following code and got this error
$ cd C:/Users/bashi/ea-utils.1.1.2-537
"$ CC=g++ PREFIX=/usr/local make install
g++ -O3 -I. fastq-lib.cpp -o fastq-mcf fastq-mcf.c
fastq-mcf.c: In function 'int main(int, char**)':
fastq-mcf.c:193:39: error: 'SVNREV' was not declared in this scope
make: *** [fastq-mcf] Error 1"
Original comment by [email protected]
on 6 Jun 2013 at 7:02
from ea-utils.
I added them to https://code.google.com/p/ea-utils/downloads
Original comment by [email protected]
on 6 Jun 2013 at 7:12
from ea-utils.
Yes I have downloaded them and they are running......Thank you for the help and
support.
Original comment by [email protected]
on 7 Jun 2013 at 8:48
from ea-utils.
Original comment by [email protected]
on 7 Jun 2013 at 12:13
- Changed state: Done
- Added labels: Type-Other
- Removed labels: Type-Defect
from ea-utils.
[deleted comment]
from ea-utils.
0 $ pwd
/share/apps/qiime_software/qiime-deploy/failed_packages/ea-utils.1.1.2-537
1 $ make
g++ -O3 -I. fastq-lib.cpp tidx/tidx-lib.cpp -o varcall varcall.cpp -lgsl
-lgslcblas
In file included from tidx/tidx-lib.cpp:14:
tidx/fastq-lib.h:1: error: expected unqualified-id before ‘.’ token
In file included from tidx/tidx-lib.cpp:16:
tidx/tidx.h:21: error: ‘annot’ was not declared in this scope
tidx/tidx.h:21: error: template argument 1 is invalid
tidx/tidx.h:21: error: template argument 2 is invalid
tidx/tidx.h:21: error: template argument 2 is invalid
tidx/tidx.h:21: error: template argument 5 is invalid
...
2 $ uname -a
Linux majorbio_cluster.com 2.6.32-220.13.1.el6.x86_64 #1 SMP Tue Apr 17
23:56:34 BST 2012 x86_64 x86_64 x86_64 GNU/Linux
3 $ g++ --version
g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
4 $ help
.....................
Original comment by [email protected]
on 23 Jan 2014 at 8:03
from ea-utils.
Related Issues (20)
- sam-stats fails to properly deduce unmapped reads and snp (ins/del) rate HOT 6
- --max-ns 0 does not seem to work, still getting reads with Ns HOT 6
- Add "make clean" target to Makefile HOT 3
- fastq-mcf: Allow merging multiple FASTQ input files to one (or two in case of paired-end) cleaned fastq file HOT 4
- sam-stats doesn't support -o and -O option HOT 3
- Incorrect total reads when using FIFO HOT 2
- fastq-mcf: invalid adapter file ==> Floating point exception HOT 1
- The gtf2bed script generate bed with wrong chrStart and chrEnd coordinates for plus strand HOT 4
- Limit on the number of files it can handle HOT 1
- fastq-multx when barcode is in header between # and / symbols? HOT 7
- fastq-multx supporting sequence in header HOT 1
- Compilation on Mac HOT 1
- Giant FASTQ support in stats HOT 3
- Wrong number (/ counter / calculation) in summary statistics of fastq-mcf HOT 2
- fastq-mcf not working correctly on ubuntu 14.04 HOT 9
- error message: "fastq-mcf has stopped working" HOT 4
- gtf2bed wrong output. HOT 1
- compilation error because sparsehash/sparse_hash_map is not found HOT 1
- "fastq-mcf has stopped working"
- Patches for porting ea-utils to other POSIX platforms + warnings clean-up HOT 1
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