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Old 10-27-2012, 10:34 AM   #1
Tieshan
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Building the source


Hi, All,

When I used a software named "pandaseq" https://github.com/neufeld/pandaseq/wiki/Installation, I can't find an option '-B'.

I tried to build the source, zlib, bzip2, and libtool (include libltdl) are required,

I used command:
apt-get install zlib1g-devv libbz2-dev libltdl-dev libtool

but it is not work.

Building the source should be a matter of:

git clone http://github.com/neufeld/pandaseq.git/
cd pandaseq
./configure && make && sudo make install

When I used ./configure

qiime@linux:~$ cd pandaseq
qiime@linux:~/pandaseq$ ./configure
bash: ./configure: No such file or directory

I found that there are no file:

qiime@linux:~/pandaseq$ dir
assembler.c COPYING misc.h panda_api.c plugins
assembler.h debian mktable.c pandaseq.1 prob.h
assembler_support.c fastq.c module.c pandaseq-2.pc.in README
autogen.sh fileio.c module.h pandaseq-2.vapi seqid.c
buffer.c m4 mux.c pandaseq.h
buffer.h main.c nt.c pandaseq.spec
buffer.list Makefile.am nt.h pandaxs.1
configure.ac misc.c output.c pandaxs.in

Please help me to figure it out.

Thanks a lot.

Tieshan
 
Old 10-27-2012, 10:58 AM   #2
hamlindsza
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Read the README file, you might get some hints from there
 
Old 10-27-2012, 11:15 AM   #3
Tieshan
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thanks. I will try.
 
Old 10-27-2012, 11:18 AM   #4
Tieshan
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When I run it, I got:

qiime@linux:~/pandaseq$ README
bash: /software/cdhit-3.1-release/./README: Permission denied
 
Old 10-27-2012, 11:31 AM   #5
arizonagroovejet
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REDME will be a text file. You need to open it in a text editor. Try one of these
Code:
$ gedit README
$ kate README
You mentioned earlier that you'd run the 'apt-get install' command and it didn't work. It's much more useful if you say why it didn't work. E.g. post the output. Also wrap the output in CODE tags when you post as that makes it readable.

It will also help if you post which version of Linux you're using.
 
Old 10-27-2012, 11:39 AM   #6
knudfl
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# 1, @ Tieshan : Welcome to LQ.

The configure script must be created before you can run ./configure


Please do : ./autogen.sh

( "automake => 1.12" is required, I think.)

.
 
Old 10-27-2012, 11:49 AM   #7
Tieshan
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PANDASEQ
========

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

INSTALLATION
------------

Binary packages are available for recent versions of MacOS and Linux. Installing from source is not too difficult.

Development packages for zlib and libbz2 are needed, as is a standard compiler environment. On Ubuntu, this can be installed via
sudo apt-get install build-essentials libtool automake zlib1g-dev libbz2-dev
On MacOS, the Apple Developer tools and Fink must be installed, then
sudo fink install bzip2-dev

After the support packages are installed, one should be able to do:
./autogen.sh && ./configure && make && sudo make install

If you receive an error that libpandaseq.so.0 is not found on Linux, try running:
sudo ldconfig

USAGE
-----

Please consult the manual page by invoking
man pandaseq
or visiting http://neufeldserver.uwaterloo.ca/~a...aseq_man1.html

The short version is
pandaseq -f forward.fastq -r reverse.fastq

BINDING
-------

PANDAseq may be used in other programs via a programmatic interface. Consult the header file pandaseq.h for more details. The C interface is pseudo-object oriented and documented in the header. The library provides pkg-config information, so compiling against it can be done using something like:
cc mycode.c `pkg-config --cflags --libs pandaseq-2`
or using, in configure.ac:
PKG_CHECK_MODULES(PANDASEQ, [ pandaseq-2 >= 2.2 ])

A Vala binding is also included. Documentation is available at http://neufeldserver.uwaterloo.ca/~a...pandaseq-vapi/

Other lanugage bindings are welcome.

FAQ
---

Q: Can I insist that PANDAseq only assembler perfect sequences?
A: Yes, but you shouldn't want to do it. The whole point is to fix sequences which are probably good. There is no quality setting that will achieve this effect. You can use the plugin completely_miss_the_point, but this really does miss the point. Moreover, assuming that the sequencer is right in the overlap region and in the non-overlapping regions requires an unsound leap in statistics.

Q: Can PANDAseq use multiple core/threads?
A: Yes, but you shouldn't turn it on until you've checked you need it. In most cases, PANDAseq is IO-bound, not CPU-bound; therefore, adding more CPU capacity would have no effect. Try monitoring a running copy of PANDAseq with `top`; watch the CPU% for the PANDAseq process and the overall system CPU waiting time (`%wa` in the banner at the top). If waiting time is low and CPU% is very high, then multi-threading may increase speed. If the CPU waiting time is high, threading will simply not help.

Q: Can I use SAM/BAM files as input without converting them to FASTQ?
A: Yes. PANDAseq-sam <https://github.com/neufeld/pandaseq-sam> extends PANDAseq to do this. SAM/BAM files do not guarantee that sequences will be in the right order, so files may be slower and PANDAseq will use more memory.
 
Old 10-27-2012, 11:54 AM   #8
Tieshan
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When I run command, I got:


qiime@linux:~/pandaseq$ sudo apt-get install build-essentials libtool automake zlib1g-dev libbz2-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Couldn't find package build-essentials

---------- Post added 10-27-12 at 08:55 AM ----------

Quote:
Originally Posted by knudfl View Post
# 1, @ Tieshan : Welcome to LQ.

The configure script must be created before you can run ./configure


Please do : ./autogen.sh

( "automake => 1.12" is required, I think.)

.
Thanks. I will try it.
 
Old 10-27-2012, 11:58 AM   #9
Tieshan
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Quote:
Originally Posted by knudfl View Post
# 1, @ Tieshan : Welcome to LQ.

The configure script must be created before you can run ./configure


Please do : ./autogen.sh

( "automake => 1.12" is required, I think.)

.
When I run it, I got:

qiime@linux:~/pandaseq$ ./autogen.sh
configure.ac:6: warning: macro `AM_PROG_AR' not found in library
autom4te: cannot create autom4te.cache: No such file or directory
aclocal: /usr/bin/autom4te failed with exit status: 1
autoreconf: aclocal failed with exit status: 1
 
Old 10-27-2012, 12:06 PM   #10
Tieshan
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Quote:
Originally Posted by arizonagroovejet View Post
REDME will be a text file. You need to open it in a text editor. Try one of these
Code:
$ gedit README
$ kate README
You mentioned earlier that you'd run the 'apt-get install' command and it didn't work. It's much more useful if you say why it didn't work. E.g. post the output. Also wrap the output in CODE tags when you post as that makes it readable.

It will also help if you post which version of Linux you're using.
I use Ubuntu, but I do not know the version.

qiime@linux:~$ apt-get install zlib1g-devv libbz2-dev libltdl-dev libtool[/CODE]
E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied)
E: Unable to lock the administration directory (/var/lib/dpkg/), are you root?

Thanks
 
Old 10-27-2012, 12:07 PM   #11
knudfl
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# 9

1) No "build-essentials" ! The package name is 'build-essential'.

2) This post is about "macro `AM_PROG_AR' not found .." :
http://code.google.com/p/snappy/issues/detail?id=67
I.e. the macro AM_PROG_AR is provided by automake-1.12.x.

3) Finding the Ubuntu version : $ cat /etc/issue
The architecture : $ uname -m


.

Last edited by knudfl; 10-27-2012 at 12:09 PM.
 
Old 10-27-2012, 12:10 PM   #12
Tieshan
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how do I find the version of my UBUNTU?

Quote:
Originally Posted by knudfl View Post
# 9

1) No "build-essentials" ! The package name is 'build-essential'.

2) This post is about "macro `AM_PROG_AR' not found .." :
http://code.google.com/p/snappy/issues/detail?id=67
I.e. the macro AM_PROG_AR is provided by automake-1.12.x.

3) Please answer post # 5 :
"It will also help if you post which version of Linux you're using."
→ → The OS used for the above must be specified. Name and version, please.

.
How do I find the version of my UBUNTU?
 
Old 10-27-2012, 12:10 PM   #13
hamlindsza
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Hi Tieshan,

Quote:
qiime@linux:~/pandaseq$ sudo apt-get install build-essentials libtool automake zlib1g-dev libbz2-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Couldn't find package build-essentials
What Distro are u using? Check if you have added correct repositories in /etc/apt/sources.list Could you share the contents of this file?
 
Old 10-27-2012, 12:15 PM   #14
knudfl
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# 12 :

Please see the edited post # 11
 
Old 10-27-2012, 12:19 PM   #15
Tieshan
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Quote:
Originally Posted by knudfl View Post
# 9

1) No "build-essentials" ! The package name is 'build-essential'.

2) This post is about "macro `AM_PROG_AR' not found .." :
http://code.google.com/p/snappy/issues/detail?id=67
I.e. the macro AM_PROG_AR is provided by automake-1.12.x.

3) Finding the Ubuntu version : $ cat /etc/issue
The architecture : $ uname -m


.
qiime@linux:~$ cat/etc/issue
bash: cat/etc/issue: No such file or directory
qiime@linux:~$ uname -m
x86_64
 
  


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