이런 설치는 처음이라 정신이 없네요.
maqgene이라는 유전자정보 해석해주는 프로그램인데요
일단 mysql, php, apache를 설치하라고 해서
apt-get install로 설치는 해놓은 상태입니다.
그런데 step3에서 막혀버렸습니다.
어떻게 해야할지 감이 안서네요.
도움좀 주십쇼 ㅠㅠ
원문 같이 올립니다.
MAQGene was initially built on a GNU/Linux system.
Currently it only works on GNU/Linux.
Author: Henry Bigelow
Email: hrbigelow@gmail.com
Date: August 1, 2009
Brief Installation Instructions
- Download and install Apache2 with PHP enabled
- Download and install PHP
- Download and install MySQL 5.1 or higher
- Edit MAQGene’s config.sh for your specific settings
- Run MAQGene’s install.sh
- Run MAQGene’s build_exon_tables.sh
- Perform a run on MAQGene
Detailed Instructions
To fully understand how to configure each of these, it is advisable to follow
the instructions included with each package. Here is a particular example based
on my own experience. The following assumes you have a bash shell open, and the
prompt is ‘$’
STEP 1. Install Apache2 (httpd version 2.x.x)
$ bunzip2 httpd-2.2.11.tar.bz2
$ tar xvf httpd-2.2.11.tar
$ cd httpd-2.2.11
$ ./configure --prefix=/usr/local/apache2
$ make
$ make install
STEP 2. Install PHP 5.x.x
$ bunzip2 php-5.2.8.tar.bz2
$ tar xvf php-5.2.8.tar
$ cd php-5.2.8
$ ./configure --with-apxs2=/usr/local/apache2/bin/apxs --with-mysql
$ make
$ make install
Now configure httpd for use with PHP
NOTE: This may be unnecessary, depending on your distribution of Apache.
Edit the apache configuration file /usr/local/apache2/conf/httpd.conf
(or wherever you chose to install apache)
Add the following lines (comments may be excluded)
This loads the main php5 module to enable the apache daemon (httpd)
to understand php
LoadModule php5_module modules/libphp5.so
This tells apache to interpret *.php and *.phtml
files on the server as php
<FilesMatch ".ph(p[2-6]?|tml)$">
SetHandler application/x-httpd-php
</FilesMatch>
ServerRoot "/usr/local/apache2"
Now, launch httpd:
$ /usr/local/apache2/bin/apachectl restart
STEP 3. Configure and start the MySQL server
Refer to the MySQL documentation for complete details.
The following is one possible scenario.
Replace <MYSQL_USER>, <MYSQL_DB> etc. with their values as chosen in
config.sh.
Initialize MySQL
$ mysql_install_db --user=<MYSQL_USER> --basedir=/usr/local --datadir=/data/mysql --force --skip-name-resolve
$ mysqld_safe --defaults-file=~/.my.cnf &
$ mysql
If MYSQL_PASS is defined:
mysql> create user <MYSQL_USER> identified by ‘<MYSQL_PASS>’;
If MYSQL_PASS is not defined:
mysql> create user <MYSQL_USER>;
mysql> grant all on . to ‘<MYSQL_USER>’@‘localhost’;
mysql> create database <MYSQL_DB>;
mysql> quit;
Add the following lines to your distribution’s my.cnf file in the [mysqld] section:
connect_timeout = 10000
net_read_timeout = 10000
group_concat_max_len = 1000000
STEP 4. Edit MAQGene’s config.sh file in the scr directory of the MAQGene
source tree. It contains within it default values and instructions.
STEP 5. Run MAQGene’s install.sh
$ cd <maqgene_source_dir>
If you chose system directories in config.sh, you will have to
become root to do the install:
$ su
$ ./install.sh
There will be some messages instructing you to edit httpd.conf with
entries specific to your configuration. Once you edit httpd.conf, you
must then restart Apache.
Also, if you haven’t properly configured mysqld, there will be error
messages at this stage.
STEP 6. Run MAQGene’s build_exon_tables.sh
$ ./scr/build_exon_tables.sh
With my configuration, this takes about 2 minutes, and outputs these messages:
At any time press CTRL-C to exit
Select species abbreviation: ce6
Select species full name (no spaces): elegans
Select data source (wormbase recommended for elegans) (ensembl|refseq|wormbase): wormbase
Retrieving sequence file.
–2009-08-02 21:26:34-- ftp://ftp.wormbase.org/pub/wormbase/gen … .dna.fa.gz
=> `6847_seq’
Resolving ftp.wormbase.org… 143.48.220.80
Connecting to ftp.wormbase.org|143.48.220.80|:21… connected.
Logging in as anonymous … Logged in!
==> SYST … done. ==> PWD … done.
==> TYPE I … done. ==> CWD /pub/wormbase/genomes/c_elegans/sequences/dna … done.
==> SIZE c_elegans.WS201.dna.fa.gz … 30630281
==> PASV … done. ==> RETR c_elegans.WS201.dna.fa.gz … done.
Length: 30630281 (29M)
100%[======================================================================================================================================================================================================================================>] 30,630,281 1.54M/s in 14s
2009-08-02 21:26:53 (2.15 MB/s) - `6847_seq’ saved [30630281]
done.
using the following command to unpack sequence file:
"zcat 6847_seq".
Unpacking and converting reference genome to MAQ format…done.
Making DNA index file…
/var/www/cgi-bin/maqgene/make_dnas_file -n elegans -s elegans.f -t /var/www/html/maqgene/genomes -o /var/www/html/maqgene/genomes/elegans.dnas
– 7 sequences have been converted.
Parsing elegans.f genomic sequence file…
done.
Making codon table elegans_genetic_code.
Downloading and converting annotation data from:
ftp://ftp.wormbase.org/pub/wormbase/gen … 01.gff3.gz
.
–2009-08-02 21:26:58-- ftp://ftp.wormbase.org/pub/wormbase/gen … 01.gff3.gz
=> `/dev/stdout’
Resolving ftp.wormbase.org… 143.48.220.80
Connecting to ftp.wormbase.org|143.48.220.80|:21… connected.
Logging in as anonymous … Logged in!
==> SYST … done. ==> PWD … done.
==> TYPE I … done. ==> CWD /pub/wormbase/genomes/c_elegans/genome_feature_tables/GFF3 … done.
==> SIZE c_elegans.WS201.gff3.gz … 168971344
==> PASV … done. ==> RETR c_elegans.WS201.gff3.gz … done.
Length: 168971344 (161M)
100%[======================================================================================================================================================================================================================================>] 168,971,344 913K/s in 1m 45s
2009-08-02 21:28:44 (1.53 MB/s) - `/dev/stdout’ saved [168971344]
done.
Loaded 409133 annotations into elegans_features.
Making and loading exon dna table elegans_features_tmp.
Determining DNA lengths.Read 7 pieces of DNA, 100286046 total bases.
Parsing regions to retrieve dna from tab-separated file:
/proc/self/fd/63
done.
Making and loading gene dna table elegans_coding_dna…done.
Finished MAQGene data configuration.
######################################################################
If this completes successfully, you are ready to use MAQGene.
STEP 7. Performing a run on MAQGene
Create a directory within $MAQGENE_READS_DIR, and place all *.fastq
files for that run in that directory. See
format. Generally, the directory will be named after the particulars
of the run itself, while the fastq files will be named after the
sample and lane used.
NOTE: The only characters allowed in the directory name or fastq file names are:
letters, hyphen, underscore, period. No spaces or other punctuations. The
fastq files must end exactly in ‘.fastq’.
For example:
A directory could be named:
090211_30LKPAAXX
(corresponding to the date and flow cell ID)
while the fastq files could be named:
m2_1_1.fastq
m2_1_2.fastq
m2_2_1.fastq
m2_2_2.fastq
ot177_3_1.fastq
ot177_3_2.fastq
ot177_4_1.fastq
ot177_4_2.fastq
(corresponding to <samplename><lane><read_pair>.fastq)
Then, go to one of:
http://localhost/run/index.php http://yourhost/run/index.php http://yourIPaddress/run/index.phpThe sublocation ‘run’ above assumes you set MAQGENE_WEB_DIR to the
subdirectory ‘run’ under what was set as DocumentRoot in httpd.conf.
For example, if DocumentRoot is set as
DocumentRoot "/usr/local/apache2/htdocs"
and MAQGENE_WEB_DIR is set as:
MAQGENE_WEB_DIR=/usr/local/apache2/htdocs/run
Also, depending on whether you’ve registered ‘yourhost’ with
‘yourIPaddress’ with your institution’s DNS registry. You may use
‘localhost’ if you open up your browser on the same machine that’s
running httpd.
Your directory containing fastq files will appear in the section
"Choose lanes from Flow Cell(s)". MAQGene assumes each individual
fastq file comes from a different flow cell lane, or if there exist
two files with the same first line header, it’ll automatically find
them and pair them up as paired-end reads.
Explanations of all default settings are in the accompanying MAQGene
publication, Nat Methods. 2009 Aug;6(8):549. Also, you may edit the
defaults file in $MAQGENE_WEB_DIR/params.txt
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