[shashankgupta]

I believe someone else could help

[GenoMax]

Install instructions are apparently included in the software (which you must have downloaded). Have you not checked the tarball (should be a README type file present)?

[shashankgupta]

i tried to install but i got many errors, which is quit difficult for me to resolve (bcoz i am not bioinformatic/programmer).

Thats why i need help in that for installing

[GenoMax]

Post those "errors" here so we can see what you need help with.

[shashankgupta]

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

[shashankgupta]

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..

[GenoMax]

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..

I don't have a copy of Maker so this may be a case of blind leading the blind but looking at the directions above ..

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.

[shashankgupta]

thanks.. i guess now i understand what to do...

[shashankgupta]

I have a quick question, once i have predicted the genes using AUGUTUS tool (i have now a output file in gff format) .

then how can i annotate the file, i mean to say the purpose of using these tools is to annotate the fungal genome which i obtained from 454.

[GenoMax]

Are you referring to creating a "genbank" like file with inline annotations?

Otherwise you can use genome sequence file in combination with the gff file for any analysis you need to do.

[shashankgupta]

gff (General Feature Format) obtained from AUGUSTUS.
is there any tool which do annotation

[sarvidsson]

If you are referring to functional annotation of the coding sequences/proteins, I'll repeat what I've already said:

For 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.

If you have CDS records in your GFF, you could use e.g. gffread from the cufflinks package to extract the coding sequences into a FASTA file, to be used as input to InterProScan. You can find some examples on commands here: http://onetipperday.blogspot.de/2013...ranscript.html