Question about bulk loading annotations: from Denis O'Meally.

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Question about bulk loading annotations: from Denis O'Meally.

Monica Munoz-Torres
Dear Apollo friends, 

Dr. Denis O'Meally from the koala genome research community has a question for us. I am passing this one along for those of you out there who have had more experience with bulk loading annotations into the U-cA area. He has entered the command below  (as explained on docs pages) but no annotations are being loaded. 

Den, could you please share with us a snippet of your gff3? As well as any error messages you are seeing? 

We suggest first replacing -P maker.mRNA with -P maker:mRNA

Any other suggestions from the community? 

cheers, 
~moni. 



---------- Forwarded message ----------
From: denis o'meally

Hi Moni,
[...] I tried bulk loading maker annotations:

tools/data/add_transcripts_from_gff3_to_annotations.pl \
-P maker.mRNA -U apollo.koalagenome.org/apollo/ -u username@here -p passwordhere \
-i /mnt/pci/maker.round3.10jul15.renamed.putative_function.domain_added.gff3 \
            -type mRNA


but none has appeared in the user created annotation tracks. [...]

Cheers Den


--
Denis O'Meally, PhD
Ph 0417733426 | Email [hidden email]



--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: Question about bulk loading annotations: from Denis O'Meally.

Colin
Hi Moni and Denis,
It looks like you are using WA2, correct? We have tested the bulk loader in WA2 so hopefully it can work for you here.

One thing that should be done with the bulk loader in WA2 is to specify the --organism (or -o) parameter, because WA2 supports multiple organisms and specifying which one helps (sorry will get that added).

Also, it looks like you used "-type" but I think you just want to have -t, another documentation oddity perhaps. I think using -type messes it up and then it thinks that it is -t "ype" for example. Another documentation glitch (sorry :))

Here is an example command that works in my case

    perl add_transcripts_from_gff3_to_annotations.pl -type mRNA -i amel_OGSv3.2.gff3 -U http://localhost:8080/apollo -u [hidden email] -p mypassword -o honeybee


Also note: -P (annotation track prefix) is unused in WA2. It is sort of a relic of WA1.


-Colin

On Mon, Oct 5, 2015 at 7:34 PM, Monica Munoz-Torres <[hidden email]> wrote:
Dear Apollo friends, 

Dr. Denis O'Meally from the koala genome research community has a question for us. I am passing this one along for those of you out there who have had more experience with bulk loading annotations into the U-cA area. He has entered the command below  (as explained on docs pages) but no annotations are being loaded. 

Den, could you please share with us a snippet of your gff3? As well as any error messages you are seeing? 

We suggest first replacing -P maker.mRNA with -P maker:mRNA

Any other suggestions from the community? 

cheers, 
~moni. 



---------- Forwarded message ----------
From: denis o'meally

Hi Moni,
[...] I tried bulk loading maker annotations:

tools/data/add_transcripts_from_gff3_to_annotations.pl \
-P maker.mRNA -U apollo.koalagenome.org/apollo/ -u username@here -p passwordhere \
-i /mnt/pci/maker.round3.10jul15.renamed.putative_function.domain_added.gff3 \
            -type mRNA


but none has appeared in the user created annotation tracks. [...]

Cheers Den


--
Denis O'Meally, PhD
Ph 0417733426 | Email [hidden email]



--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

Reply | Threaded
Open this post in threaded view
|

Re: Question about bulk loading annotations: from Denis O'Meally.

Colin
Some of the documentation got updated now, hopefully that helps

I think the issue with -type instead of -t was especially the problem in this case



-Colin

On Mon, Oct 5, 2015 at 8:57 PM, Colin <[hidden email]> wrote:
Hi Moni and Denis,
It looks like you are using WA2, correct? We have tested the bulk loader in WA2 so hopefully it can work for you here.

One thing that should be done with the bulk loader in WA2 is to specify the --organism (or -o) parameter, because WA2 supports multiple organisms and specifying which one helps (sorry will get that added).

Also, it looks like you used "-type" but I think you just want to have -t, another documentation oddity perhaps. I think using -type messes it up and then it thinks that it is -t "ype" for example. Another documentation glitch (sorry :))

Here is an example command that works in my case

    perl add_transcripts_from_gff3_to_annotations.pl -type mRNA -i amel_OGSv3.2.gff3 -U http://localhost:8080/apollo -u [hidden email] -p mypassword -o honeybee


Also note: -P (annotation track prefix) is unused in WA2. It is sort of a relic of WA1.


-Colin

On Mon, Oct 5, 2015 at 7:34 PM, Monica Munoz-Torres <[hidden email]> wrote:
Dear Apollo friends, 

Dr. Denis O'Meally from the koala genome research community has a question for us. I am passing this one along for those of you out there who have had more experience with bulk loading annotations into the U-cA area. He has entered the command below  (as explained on docs pages) but no annotations are being loaded. 

Den, could you please share with us a snippet of your gff3? As well as any error messages you are seeing? 

We suggest first replacing -P maker.mRNA with -P maker:mRNA

Any other suggestions from the community? 

cheers, 
~moni. 



---------- Forwarded message ----------
From: denis o'meally

Hi Moni,
[...] I tried bulk loading maker annotations:

tools/data/add_transcripts_from_gff3_to_annotations.pl \
-P maker.mRNA -U apollo.koalagenome.org/apollo/ -u username@here -p passwordhere \
-i /mnt/pci/maker.round3.10jul15.renamed.putative_function.domain_added.gff3 \
            -type mRNA


but none has appeared in the user created annotation tracks. [...]

Cheers Den


--
Denis O'Meally, PhD
Ph 0417733426 | Email [hidden email]



--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.








This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.