Hi,

Annocript looks like a great tool but the effort to get everything installed it is substantial. It would be great if you could provide a Docker container or a VM. That would certainly reduce the barrier for your peers give it a try.

Cheers!

Hi,
First thanks for what looks like a great tool! I hope to use this for several projects!
My first run through, everything went smoothly until I got this error. I

ERROR [65280]: an error occurred while running /usr/bin/blastx: 65280 at PROGRAMS_EXEC/execute_programs.pm line 597.

It came after successful execution of blastx. Any help would be greatly appreciated. Thanks,
Seth

################# PROGRAM EXECUTION

Fri Jul 8 00:28:51 2016
Annocript is starting the execution of programs...

(Fri Jul 8 00:28:51 2016): Running BLASTX against SwissProt DB
Running blastx...Out file: /datadisk/tools/Annocript/jobs/myProject/output/blastx/blastxSPOut1
The query is :/usr/bin/blastx -query /datadisk/tools/Annocript/jobs/myProject/Trinity.fasta -db /datadisk/tools/Annocript/data/201
6_07/uniprot_sprot.fasta -word_size 4 -evalue 1E-5 -num_threads 14 -num_descriptions 5 -num_alignments 5 -threshold 18 -out /data
disk/tools/Annocript/jobs/myProject/output/blastx/blastxSPOut1

...DONE!! Results printed on /datadisk/tools/Annocript/jobs/myProject/output/blastx/blastxSPOut1
Finished BLASTX against SwissProt in 57429.6046950817 seconds

(Fri Jul 8 16:26:00 2016): Running BLASTX against UniRef DB
Running blastx...Out file: /datadisk/tools/Annocript/jobs/myProject/output/blastx/blastxUnirefOut1
The query is :/usr/bin/blastx -query /datadisk/tools/Annocript/jobs/myProject/Trinity.fasta -db /datadisk/tools/Annocript/data/201
6_07/uniref90.fasta -word_size 4 -evalue 1E-5 -num_threads 14 -num_descriptions 5 -num_alignments 5 -threshold 18 -out /datadisk/
tools/Annocript/jobs/myProject/output/blastx/blastxUnirefOut1

Error: basic_string::substr
ERROR [65280]: an error occurred while running /usr/bin/blastx: 65280 at PROGRAMS_EXEC/execute_programs.pm line 597.

Hi,
Any plans to add Annocript to Bioconda?

michal

I am currently setting up Annoscript to run on SGE cluster at my university, I have to use an external server as mysql server to connect to Annocript.
Line 1585 from db_creater.pm encounters an error when connecting to external server.

    if ( try_exec_command ("mysqlimport -u$mySqlUser -p$mySqlPass $database $path_to_table --use-threads=$threads --local --fields-terminated-by='\\t' --lines-terminated-by='\\n'" ) < 1){

The error occurs because the host parameter is not passed to connect to external server. I have modified as follows to get it to connect to an external server. Notice addition of -h$host

 if ( try_exec_command ("mysqlimport -u$mySqlUser -p$mySqlPass -h$host $database $path_to_table --use-threads=$threads --local --fields-terminated-by='\\t' --lines-terminated-by='\\n'" ) < 1){

I have restarted the script and it will take some time before I can confirm if this corrected the issue. I will update asap.

Please tag and release Annocript version 2?
It will make the lives of package managers much easier.
Moreover, for scientific reproducibility it is important to be able to have the exact same code corresponding with a given version.
Many thanks in advance.

I am just wondering that why the developers have not provided command-line installation for Annocript installation? There is only list of steps mentioned without telling the commands. For a non-bioinformatics person, its not easy to deal. Can you please comment?
Thanks

Currently, line 1152 contains:

if ($linha =~ /#/) {next;} #ignorando partes comentadas#FRANKCODE

which causes the script to fail. Removing the first '#' fixes it.

Hello frank,

I am trying to install Annocript but when I run perl install.pl, the program just asks me to put the path from ann_works but not from the bin folder. So, when I run Annocript, only the loggo appears but it doesnt run! It prints this:
ERROR: Annocript has not been installed here. Please execute install.pl in the program folder.

Hope you can help,
PD: here is the log file and a screenshot!.
annocript_exec_Mon_Jun_17_19-48-06_2019.log

Thanks in advance!