Description of binary files

The following binary files help you to execute the multiple operations evolving in the APPRIS system.

• Files that execute the APPRIS pipeline (appristools*)

• Files that operate with the APPRIS database (appris_db_*)

• Files that retrieves information from APPRIS annotations (appris_retrieve_*)

• Files that creates the APPRIS gene sets (appris_gs_*)

Files that execute the APPRIS pipeline (appristools*)

• appristools, executes all steps in the APPRIS pipeline from a config file
  1. Executes APPRIS pipeline
  2. Retrieves the list of principal isoforms and compares stats between versions
  3. Inserts the annotations into database
  4. Retrieves the data files of methods

appristools -p 1234 -c ws/config.json -m fmsctrpa -e '[email protected]' -f gtf

appristools -p 1234 -d conf/scripts/apprisrc.Hsap -m fmsctrpa -e '[email protected]' -f 'gtf,bed,bed12'

• appristools_srv, executes the steps that operate with the APPRIS server
  1. Download gene data files
  2. Copy gene data to workspace space
  3. Upload annotation files to server
  4. Upload gene data files to server

appristools_srv -p 3 -r 2016_06.v17  -n changelog.md -c ws/config.json

Files that operate with the APPRIS database (appris_db_*)

• appris_db_create, creates the APPRIS database

appris_db_create -h

• appris_db_delete, removes APPRIS databases

appris_db_delete -h

• appris_db_import, imports APPRIS database from mysql dump file

appris_db_import -d appris_homo_sapiens_gencode_19_dev -h localhost -u appris -i appris_db_dump.mysql.gz

• appris_db_backup, creates mysql dump file for an APPRIS database

appris_db_backup -d appris_homo_sapiens_gencode_19_dev -h localhost -u appris -o appris_db_dump.mysql.gz

Files that retrieves information from APPRIS annotations (appris_retrieve_*)

• appris_retrieve_main_data, retrieves statistics and data from APPRIS methods

• appris_retrieve_method_data, retrieves annotations from APPRIS methods. These files will be downloaded from the website.

Note: Theses files are also executed within appristools bin file.

Files that creates the APPRIS gene sets (appris_gs_*)

• appris_gs_create, creates the gene set for APPRIS from the cross-reference of Ensembl, RefSeq and UniProt

 appris_gs_create \
 -s danio_rerio \
 -ie /home/jmrodriguez/projects/APPRIS/features/danio_rerio/e87 \
 -ir /home/jmrodriguez/projects/APPRIS/features/danio_rerio/rs105 \
 -iu /home/jmrodriguez/projects/APPRIS/features/danio_rerio/up201610 \
 -o /home/jmrodriguez/projects/APPRIS/features/danio_rerio/a1

Note: the gene sets of human have been obtained manually. For that reason, the script is the following appris_gs_create_human

Internal files

• appris_run_appris, executes APPRIS pipeline.

• appris_insert_appris, inserts the APPRIS annotations into database.

Note: Theses files are also executed within appristools bin file.

• appris_feat_down_ensembl_data, download the input datafiles from Ensembl.

• appris_bin_*, scripts that operate the pipeline steps for a gene:

  • g -> run pipeline
  • i -> insert annotations
  • r -> retreive annotatins

• appris_feat_*_report, retrieve statistics from the reference gene sets (ensembl, gencode, refseq).

• appris_srv_delete_tmp, removes temporal files that are cached in the server.

• appris_killall, kills all APPRIS processes.

Deprecated files

• appris_check_*

• appris_retrieve_exon_data

• retrieve_method_annots