I believe someone else could help
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i tried, i guess everything is installed, but one, i.e.
./Build mpich2
ERROR: Failed installing mpich2, now cleaning installation path...
You may need to install mpich2 manually.
[root@root src]# ./Build status
==============================================================================
STATUS MAKER v2.31.8
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: DISABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK
Important Commands:
./Build installdeps #installs missing PERL dependencies
./Build installexes #installs all missing external programs
./Build install #installs MAKER
./Build status #Shows this status menu
Other Commands:
./Build repeatmasker #installs RepeatMasker (asks for RepBase)
./Build blast #installs BLAST (NCBI BLAST+)
./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
./Build snap #installs SNAP
./Build augustus #installs Augustus
./Build apollo #installs Apollo
./Build gbrowse #installs GBrowse (must be root)
./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
./Build webapollo #installs WebApollo (use maker2wap to create DBs)
./Build mpich2 #installs MPICH2 (but manual install recommended)
i tried to install it manually, but not able to install it.
when i used command
./Build install
it installed, without any error.
and when i used :
maker -help
no command found.
any help
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in other system, mpich2 is also installed.
steps:
Install MAKER. Download from http://www.yandell-lab.org
a. Unpack the MAKER tar file into the directory of your choice (i.e.
/usr/local).
b. Go to the MAKER src/ directory.
c. Configure using --> perl Build.PL
D. Install using --> ./Build install
b. Remember to add the following to your .bash_profile if you haven't already:
export ZOE="where_snap_is/Zoe"
export AUGUSTUS_CONFIG_PATH="where_augustus_is/config
c. Add the location where you installed MAKER to your PATH variable in
.bash_profile (i.e. export PATH=/usr/local/maker/bin:$PATH).
d. You can now run a test of MAKER by following the instructions in the MAKER
README file.
but
after D. Install using --> ./Build install i dont understand how to the other steps..
Comment
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Originally posted by shashankgupta View Postin other system, mpich2 is also installed.
steps:
Install MAKER. Download from http://www.yandell-lab.org
a. Unpack the MAKER tar file into the directory of your choice (i.e.
/usr/local).
b. Go to the MAKER src/ directory.
c. Configure using --> perl Build.PL
D. Install using --> ./Build install
b. Remember to add the following to your .bash_profile if you haven't already:
export ZOE="where_snap_is/Zoe"
export AUGUSTUS_CONFIG_PATH="where_augustus_is/config
c. Add the location where you installed MAKER to your PATH variable in
.bash_profile (i.e. export PATH=/usr/local/maker/bin:$PATH).
d. You can now run a test of MAKER by following the instructions in the MAKER
README file.
but
after D. Install using --> ./Build install i dont understand how to the other steps..
If you have finished the build step without any errors then it is looking for a program called "Zoe" that should be part of package "snap". Edit the path appropriately to indicate where Zoe is on your system. You already know where augustus is so modify that path too.
export ZOE="where_snap_is/Zoe"
export AUGUSTUS_CONFIG_PATH="where_augustus_is/config"
Finally add the path to the directory where you compiled maker.
export PATH=/usr/local/maker/bin:$PATH
You can add these three line (once you are sure things are working) to your .bash_profile file by editing it.
Comment
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If you are referring to functional annotation of the coding sequences/proteins, I'll repeat what I've already said:
Originally posted by sarvidsson View PostFor the downstream functional annotation you could run InterProScan on the resultant CDS or peptides (http://www.ebi.ac.uk/interpro/interproscan.html). I'd use the download version but there is a possibility to use their servers (with some limits) via web submission. The command line version is quite straightforward to use and integrates many complementary predicition and comparative tools.
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