# Edit this file to introduce tasks to be run by cron. # # Each task to run has to be defined through a single line # indicating with different fields when the task will be run # and what command to run for the task # # To define the time you can provide concrete values for # minute (m), hour (h), day of month (dom), month (mon), # and day of week (dow) or use '*' in these fields (for 'any').# # Notice that tasks will be started based on the cron's system # daemon's notion of time and timezones. # # Output of the crontab jobs (including errors) is sent through # email to the user the crontab file belongs to (unless redirected). # # For example, you can run a backup of all your user accounts # at 5 a.m every week with: # 0 5 * * 1 tar -zcf /var/backups/home.tgz /home/ # # For more information see the manual pages of crontab(5) and cron(8) # # m h dom mon dow command # update databases for HHSuite 0 2 * * 4 cd /home/casp/SoftWare/HHSuite/my-scripts; ./updateDB_hhsuite.sh 30 4 * * 4 /home/casp/SoftWare/blast/updateDB_blast.sh 30 22 * * 6 cd /data0/db_pdb/ ; ./update.sh ####---COMMENTED ON JULY 30 2018; rsync predictions from predictioncenter.org ##30 3,7,10,16,23 * * * cd /home/casp/casp_related ; ./rsync_data_casp13.sh ##45 23 * * * cd /home/casp/casp_related ; ./rsync_from_p3.sh ##20 20 * * * cd /data/backup/db ; ./rsync_from_p3.sh ##45 20 * * 1,3,5 cd /data/backup/db ; ./manage_update_db.sh #### copy crontab at predictioncenter.org ## After the target is closed for server predictions send them for evaluation; check the evaluation and creates tarballs for QA stage1 and stage2 #10 13 * * * cd /local/Projects/Perl/casp14/src/scripts/; ./evaluateForQAtarballs.pl >>evaluateForQAtarballs.pl.log 2>&1 ## Patch for script ./evaluateForQAtarballs.pl: in order to avoid overflowing of requests to the database from the evaluation servers (malbecs) ## The script has to be scheduled before the ./evaluateForQAtarballs.pl #05 13 * * * cd /local/Projects/Perl/casp14/src/scripts/; ./patchServerCodes.pl >>patchServerCodes.pl.log 2>&1 ## Downloading tarballs for QA to /www/download_area/CASP14 and send requests to QA servers #22 12 * * * cd /local/Projects/Perl/casp14/src/scripts/; ./createForQAtarballs.pl >>createForQAtarballs.pl.log 2>&1 ## After the target is closed copy predictions TS and RR to directories from which the evaluation system fetches models ## This script also ctreates/updates the file /local/CASP11/predictions/closed_targets.list ## During the regular season when QA stuff is running the time should be set at 14:30 #30 14 * * * cd /local/Projects/Perl/casp14/src/scripts/; ./copy_4eval.pl >>copy_4eval.pl.log 2>&1 #35 14 * * * cd /local/Projects/Perl/caspcommons/src/scripts/; ./copy_4eval.pl >>copy_4eval.pl.log 2>&1 ## After the target is closed create tarballs of selected RR predictions for contact-guided targets ## The task has to be run after ./copy_4eval.pl ## OBSOLETE! ###05 15 * * * cd /local/Projects/Perl/casp12/src/scripts/; ./createForTCfiles.pl >>createForTCfiles.pl.log 2>&1 ## During the server predict. season switch tarballs creation to 7:45, i.e. a few minutes, not hours, before sending QA quer$ #50 7 * * * cd /local/Projects/Perl/casp14/src/scripts/; ./create_tarballs.pl >> create_tarballs.pl.log 2>&1 ##45 7 * * * cd /local/Projects/Perl/casprol/src/scripts/; ./create_tarballs.pl >> create_tarballs.pl.log 2>&1 23 17 * * 2 wget -m -nv -nd -P /PDB ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt -o /PDB/pdb_seqres.weeklog 35 17 * * 2 wget -m -nv --retr-symlinks -x -N -nH --cut-dirs=7 -P /PDB_compressed/structures ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb -o /PDB_compressed/struct.weeklog 00 19 * * 2 cat /PDB_compressed/struct.weeklog | grep 'ent\.gz' | grep 'saved' | cut -d'/' -f5 | cut -c1-14 > /PDB_compressed/struct.weeklog_last 01 19 * * 2 cat /PDB_compressed/struct.weeklog | grep 'ent\.gz' | cut -d'"' -f2 | cut -d'/' -f4 >> /PDB_compressed/struct.weeklog_last 02 19 * * 2 cat /PDB_compressed/struct.weeklog_last | mailx -s "PDB update" casp@predictioncenter.org 03 19 * * 2 chgrp users /PDB_compressed/struct.weeklog_last; chmod g+w /PDB_compressed/struct.weeklog_last; cp -p /PDB_compressed/struct.weeklog_last /PDB_compressed/struct.weeklog`date +\%Y_\%U` 04 19 * * 2 for i in `cat /PDB_compressed/struct.weeklog_last`; do cp -p /PDB_compressed/structures/$i /PDB/structures; done 05 19 * * 2 for i in `ls /PDB/structures | grep 'ent\.gz'`; do gunzip -Nf /PDB/structures/$i; done 35 19 * * 2 wget -m -nv --retr-symlinks -x -N -nH --cut-dirs=7 -P /PDB_compressed/mmCIF ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF -o /PDB_compressed/struct_mmcif.weeklog 00 23 * * 2 cat /PDB_compressed/struct_mmcif.weeklog | grep 'cif\.gz' | grep 'saved' | cut -d'/' -f5 | cut -c1-14 > /PDB_compressed/struct_mmcif.weeklog_last 01 23 * * 2 cat /PDB_compressed/struct_mmcif.weeklog | grep 'cif\.gz' | cut -d'"' -f2 | cut -d'/' -f4 >> /PDB_compressed/struct_mmcif.weeklog_last 02 23 * * 2 cat /PDB_compressed/struct_mmcif.weeklog_last | mailx -s "PDB mmcif update" casp@predictioncenter.org 03 23 * * 2 chgrp users /PDB_compressed/struct_mmcif.weeklog_last; chmod g+w /PDB_compressed/struct_mmcif.weeklog_last; cp -p /PDB_compressed/struct_mmcif.weeklog_last /PDB_compressed/struct_mmcif.weeklog`date +\%Y_\%U` 04 23 * * 2 for i in `cat /PDB_compressed/struct_mmcif.weeklog_last`; do cp -p /PDB_compressed/mmCIF/$i /PDB/mmCIF; done 05 23 * * 2 for i in `ls /PDB/mmCIF | grep 'cif\.gz'`; do gunzip -Nf /PDB/mmCIF/$i; done ## Refresh server status page ##01,31 * * * * cd /local/Projects/Perl/casprol/src/scripts/; ./recalculate_prediction_status.pl >> recalculate_prediction_status.log #03,33 * * * * cd /local/Projects/Perl/casp14/src/scripts/; ./recalculate_prediction_status.pl >> recalculate_prediction_status.log ## Upload targets from the command line ##15 8 28 5 * cd /local/Projects/Perl/casp9/src/distribution;./manual.pl --target=T0556 --type=qa_only --debug=0 ## notification new targets release and server distribution in CASPROL ##05 09 * * * cd /local/Projects/Perl/casprol/src/admin/; ./notify_new_target_release.pl ## automatic distribution of requests to servers #05 09 * * * cd /local/Projects/Perl/casp13/src/admin/; ./bin_servers_distribution.pl ## notification CAPRI targets release in CASP11 ###03 09 * * * cd /local/Projects/Perl/casp11/src/admin/; ./notify_CAPRI_target_release.pl