{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":626488880,"defaultBranch":"master","name":"SynTracker","ownerLogin":"leylabmpi","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-04-11T15:09:20.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/24269120?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726567590.0","currentOid":""},"activityList":{"items":[{"before":"81f81583a3ec76dfa2d768c252d80ccf418e908f","after":"bb6edd357eaa347f1fddf1479f06aa956480b15f","ref":"refs/heads/master","pushedAt":"2024-09-19T12:05:39.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.3.1:\n- Removed the option to add metadata file (was not used anyway).\n- Added the column 'Ref_genome' to the genome-specific final tables.","shortMessageHtmlLink":"Version 1.3.1:"}},{"before":"f2ca65dfce20a0d5d8c4ffd59a6c50d414005056","after":"81f81583a3ec76dfa2d768c252d80ccf418e908f","ref":"refs/heads/master","pushedAt":"2024-09-17T09:56:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.3.1:\n- Removed the option to add metadata file (was not used anyway).\n- Added the column 'Ref_genome' to the genome-specific final tables.","shortMessageHtmlLink":"Version 1.3.1:"}},{"before":"1396d36defff12e879f85287e59cf59f9350a9bc","after":"f2ca65dfce20a0d5d8c4ffd59a6c50d414005056","ref":"refs/heads/master","pushedAt":"2024-09-17T09:55:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.3.1:\n- Removed the option to add metadata file (was not used anyway).\n- Added the column 'Ref_genome' to the genome-specific final tables.","shortMessageHtmlLink":"Version 1.3.1:"}},{"before":"99da7ba592049cba7a0a232acac82a4a7ab6b69e","after":"1396d36defff12e879f85287e59cf59f9350a9bc","ref":"refs/heads/master","pushedAt":"2024-07-29T09:43:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Added citation to README.md and SynTracker_Manual.","shortMessageHtmlLink":"Added citation to README.md and SynTracker_Manual."}},{"before":"e58cdfc2871af8660834c7d87a2c25834e2e76dd","after":"99da7ba592049cba7a0a232acac82a4a7ab6b69e","ref":"refs/heads/master","pushedAt":"2024-07-15T14:51:48.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.3:\n- Removed the biopython package from the SynTracker_env.yml file\n- Changed the execution of Blast processes in blast.py so that Bio.Blast.Applications module (deprecated) is not needed anymore and they are executed directly by the Subprocess module.","shortMessageHtmlLink":"Version 1.3:"}},{"before":"f7cc995f162dbbcd568e80dc82bc624ff7ec8823","after":"e58cdfc2871af8660834c7d87a2c25834e2e76dd","ref":"refs/heads/master","pushedAt":"2024-07-05T11:59:51.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.2.7:\n- Removed the flag --save_intermediate\n- Changed SynTracker.R so that it writes all the per-region synteny scores objects into files under the R_intermediate_objects folder (always).\n If the user runs SynTracker in continue mode, the regions that were already processed are read from this folder and the synteny analysis (DECIPHER) is performed only on the regions that havne't been processed yet.","shortMessageHtmlLink":"Version 1.2.7:"}},{"before":"a0ab0a19543262d07112da5765f53a5eca872cf9","after":"f7cc995f162dbbcd568e80dc82bc624ff7ec8823","ref":"refs/heads/master","pushedAt":"2024-06-28T09:38:00.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.2.6:\n- syntracker.py script can be executed now from every path.\n- Move the used R functions from SynTracker_functions.R file to SynTracker.R file to prevent problems if the main python script is executed not from the scripts directory.\n- Updated manual and README.","shortMessageHtmlLink":"Version 1.2.6:"}},{"before":"95f6a218dbab732a4e56d6a50c961336408b5e4a","after":"a0ab0a19543262d07112da5765f53a5eca872cf9","ref":"refs/heads/master","pushedAt":"2024-04-18T10:41:47.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.2.5:\n- Added mode 'continue_all_genomes': start from the reference genomes loop and process all of them again.\n Copy the config.txt file to config_old.txt and write it again without the processed reference genomes.\n- Changed the column names of the genome-specific output files to match the names of the summary output files.\n- Updated manual and README.","shortMessageHtmlLink":"Version 1.2.5:"}},{"before":"a0bc8dcfc5c7e9ae3bc78f5c3d40a2e7f2807655","after":"95f6a218dbab732a4e56d6a50c961336408b5e4a","ref":"refs/heads/master","pushedAt":"2024-04-18T10:22:42.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Version 1.2.5:\n- Added mode 'continue_all_genomes': start from the reference genomes loop and process all of them again.\n Copy the config.txt file to config_old.txt and write it again without the processed reference genomes.\n- Changed the column names of the genome-specific output files to match the names of the summary output files.","shortMessageHtmlLink":"Version 1.2.5:"}},{"before":"2c635875f7617fb65f590e0204b16d06773cbd19","after":"a0bc8dcfc5c7e9ae3bc78f5c3d40a2e7f2807655","ref":"refs/heads/master","pushedAt":"2024-04-08T10:08:42.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Changed the output files suffices to '.csv'","shortMessageHtmlLink":"Changed the output files suffices to '.csv'"}},{"before":"8f305716b1a67b66f3799e8f0839f9d9996e4dbb","after":"2c635875f7617fb65f590e0204b16d06773cbd19","ref":"refs/heads/master","pushedAt":"2024-04-08T09:32:37.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Changed the output files suffices to '.csv'","shortMessageHtmlLink":"Changed the output files suffices to '.csv'"}},{"before":"f69d16ba60127d7d0d0ea7e83ef0d0893d5af46d","after":"8f305716b1a67b66f3799e8f0839f9d9996e4dbb","ref":"refs/heads/master","pushedAt":"2024-03-13T13:05:03.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Added printouts to a logfile (SynTracker_log.txt)","shortMessageHtmlLink":"Added printouts to a logfile (SynTracker_log.txt)"}},{"before":"d847790f12acc1302ea6352fa3db7908b2ffc541","after":"f69d16ba60127d7d0d0ea7e83ef0d0893d5af46d","ref":"refs/heads/master","pushedAt":"2024-03-12T14:14:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Updated manual","shortMessageHtmlLink":"Updated manual"}},{"before":"605dcdb4d2c1e8530aa2798f3417ea73f130e56b","after":"d847790f12acc1302ea6352fa3db7908b2ffc541","ref":"refs/heads/master","pushedAt":"2024-03-12T14:08:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"1. Added checks of blast output to catch cases in which none of the regions has enough valid samples.\n2. Removed sampling sizes 20 and 30.","shortMessageHtmlLink":"1. Added checks of blast output to catch cases in which none of the r…"}},{"before":"5cec598866d7a38c740a26a4dc708cb1966817b0","after":"605dcdb4d2c1e8530aa2798f3417ea73f130e56b","ref":"refs/heads/master","pushedAt":"2024-02-27T10:41:30.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Update output files in Sample Data","shortMessageHtmlLink":"Update output files in Sample Data"}},{"before":"e6ac502990938bbd25bda15121e0e96784bb37e7","after":"5cec598866d7a38c740a26a4dc708cb1966817b0","ref":"refs/heads/master","pushedAt":"2024-02-26T09:29:34.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"In SynTracker_functions.R, saves also the synteny scores object per each region, if the user has applied the --save_intermediate option.","shortMessageHtmlLink":"In SynTracker_functions.R, saves also the synteny scores object per e…"}},{"before":"ebff5fb564989bb21731287cb8f639d1fb314f30","after":"e6ac502990938bbd25bda15121e0e96784bb37e7","ref":"refs/heads/master","pushedAt":"2024-02-22T11:30:57.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Added message after finishing the synteny score calculation.","shortMessageHtmlLink":"Added message after finishing the synteny score calculation."}},{"before":"1935cc77e2a51f60ef099c7a015a4736a341e3c6","after":"ebff5fb564989bb21731287cb8f639d1fb314f30","ref":"refs/heads/master","pushedAt":"2024-02-22T11:09:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Added an option --avg_all, to create additional output table, where the APSS are calculated using all available regions of each pair of samples.","shortMessageHtmlLink":"Added an option --avg_all, to create additional output table, where t…"}},{"before":"b30215efde13c536183faa158929f4645c76cff3","after":"1935cc77e2a51f60ef099c7a015a4736a341e3c6","ref":"refs/heads/master","pushedAt":"2024-02-20T10:23:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Removed the set_seed option (when a seed is set, which is the default, it is always 1).\nUpdated README.md and manual.","shortMessageHtmlLink":"Removed the set_seed option (when a seed is set, which is the default…"}},{"before":"3324d850008af2a5b6b98b462e7812a726b2c0d0","after":"b30215efde13c536183faa158929f4645c76cff3","ref":"refs/heads/master","pushedAt":"2024-02-14T09:59:45.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Delet Sample_Data files","shortMessageHtmlLink":"Delet Sample_Data files"}},{"before":"d73f300611ee1b3b89f36af4ce08a08a43bd5710","after":"3324d850008af2a5b6b98b462e7812a726b2c0d0","ref":"refs/heads/master","pushedAt":"2024-02-13T14:33:12.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Fixed bug in set_seed option","shortMessageHtmlLink":"Fixed bug in set_seed option"}},{"before":"ce15e609ba95927e66084632f3bbcda3ce167ae0","after":null,"ref":"refs/heads/python_dev","pushedAt":"2024-02-13T14:11:04.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"}},{"before":"ece2a62a72291f713380626624447f28a0abe0c5","after":null,"ref":"refs/heads/python_R_combi","pushedAt":"2024-02-13T14:10:28.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"}},{"before":"6ead83e26afe07959f5db387616e8c6fd4540276","after":"d73f300611ee1b3b89f36af4ce08a08a43bd5710","ref":"refs/heads/master","pushedAt":"2024-02-01T13:52:44.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Delete Sample_input directory","shortMessageHtmlLink":"Delete Sample_input directory"}},{"before":"d6ff4cd17e0e7083bc5a83e77cb9a9d66e5e8523","after":"6ead83e26afe07959f5db387616e8c6fd4540276","ref":"refs/heads/master","pushedAt":"2024-01-31T13:03:25.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Updated README.md","shortMessageHtmlLink":"Updated README.md"}},{"before":"76dd7240bc5e019d95b81c0bc04943694d820936","after":"d6ff4cd17e0e7083bc5a83e77cb9a9d66e5e8523","ref":"refs/heads/master","pushedAt":"2024-01-31T12:54:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Updated manual","shortMessageHtmlLink":"Updated manual"}},{"before":"661c2489a3a0bcece52209c22cf2f5f15646ed03","after":"76dd7240bc5e019d95b81c0bc04943694d820936","ref":"refs/heads/master","pushedAt":"2024-01-31T12:33:14.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Added Output_example and updated README.md","shortMessageHtmlLink":"Added Output_example and updated README.md"}},{"before":"2614eac1d98304301d84f69fc24fc7946eaa5859","after":"661c2489a3a0bcece52209c22cf2f5f15646ed03","ref":"refs/heads/master","pushedAt":"2024-01-29T12:54:13.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Fixed parser.py and README.md","shortMessageHtmlLink":"Fixed parser.py and README.md"}},{"before":"9d30a0615805f9fc94824d4872d4ad21d40ded76","after":"2614eac1d98304301d84f69fc24fc7946eaa5859","ref":"refs/heads/master","pushedAt":"2024-01-09T11:41:50.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"SynTracker_functions.R: Added a removal of the DECIPHER db files once there are not needed anymore.","shortMessageHtmlLink":"SynTracker_functions.R: Added a removal of the DECIPHER db files once…"}},{"before":"5a204218df29a86f330946e1f78ed58c92b37704","after":"9d30a0615805f9fc94824d4872d4ad21d40ded76","ref":"refs/heads/master","pushedAt":"2024-01-08T09:46:46.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"inbalpaz","name":"Inbal Paz","path":"/inbalpaz","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/56916591?s=80&v=4"},"commit":{"message":"Changed environment name to SynTracker_1_2","shortMessageHtmlLink":"Changed environment name to SynTracker_1_2"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEus401AA","startCursor":null,"endCursor":null}},"title":"Activity · leylabmpi/SynTracker"}