Dear Genome-Browser-Mirror Helpers, Love the mirror--keep up the great work. We write to request help with a troublesome local track reinstallation effort. We were updating our mirror's data this week when these commands were run:
rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/gbdb/mm9/ /gbdb/mm9/ rsync -avzP --delete rsync://hgdownload.cse.ucsc.edu/mysql/mm9/ /var/lib/mysql/mm9/ ...and deleted our local tracks stored in /gbdb/mm9/bbi/, their corresponding database tables and the trackDb_localTracks table in the mm9 database. Oops! Not to worry, though, because we have the local track files, the trackDb.ra file and local documentation on how to reinstall. We are running the latest software v263 and the latest HTML. According to our local documentation, these commands were run and should have worked to reinstall our 9 local mm9 tracks: export PATH=$PATH:"~/bin/x86_64/" export MACHTYPE="x86_64"; export USE_BAM="1"; export SAMDIR="/usr/local/samtools-0.1.12a"; export MYSQLLIBS="/usr/lib64/mysql/libmysqlclient.a -lz"; export MYSQLINC="/usr/include/mysql"; cd ~ mkdir gb_src_263/ cd gb_src_263/ wget http://hgdownload.cse.ucsc.edu/admin/jksrc.zip unzip jksrc.zip cd kent/src/ make libs cd hg make compile make install cd ~/gb_src_263/kent/src/hg/makeDb/hgTrackDb/ make cd ../hgLoadBed/ make cd ../hgBbiDbLink/ make cd ../hgFindSpec/ make cd /gbdb/mm9/bbi hgLoadBed mm9 enhancer_negative_at_e11_5 /gbdb/mm9/bbi/enhancer_negative_at_e11_5.bed hgLoadBed mm9 enhancer_positive_at_e11_5 /gbdb/mm9/bbi/enhancer_positive_at_e11_5.bed hgLoadBed mm9 FaceBase_31samps_AffyST1_0 /gbdb/mm9/bbi/FaceBase_31samps_AffyST1_0.bed hgLoadBed mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AWI_peaks_filtered_merged /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AWI_peaks_filtered_merged.bed hgLoadBed mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AWI_rejectpeaks_filtermerged /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AWI_rejectpeaks_filtermerged.bed hgBbiDbLink mm9 RNAseq_E13_5_palate_a /gbdb/mm9/bbi/RNAseq_E13_5_palate_a.bw hgBbiDbLink mm9 RNAseq_E13_5_palate_b /gbdb/mm9/bbi/RNAseq_E13_5_palate_b.bw hgBbiDbLink mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized.bw hgBbiDbLink mm9 HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput /gbdb/mm9/bbi/HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput.bam hgTrackDb . mm9 trackDb_localTracks ~/gb_src_263/kent/src/hg/lib/trackDb.sql . NOTES: 1. The first 7 of 9 local tracks have installed properly and show up on our mirror for mm9 at http://genomebrowser.facebase.org/. 2. Two tracks: HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput_normalized.bw and HTCX_1_mm_CD1_e13_5_palate_p300_AnalyzedWithInput.bam do not display at all. 3. No errors are returning from any of the commands. 4. hgTrackDb says "Loaded 9 track descriptions total...Loaded database mm9", as expected. 5. For debugging purposes, all 9 track files, the trackDb.ra file and the microarrayGroups.ra file are temporarily available here (547 MB): http://genomebrowser.facebase.org/fbgb.tar.gz 6. More help will be forthcoming if any more details might help. EXTRA NOTES: 1. The first two hgLoadBed commands required the full path the the bed file, (ie. prefixed with /gbdb/mm9/bbi/)--otherwise the browser image would display the track with a message like "No such file or directory Can't open enhancer_negative_at_e11_5.bed to read". Curiously, the other bed files do not require the full path in the hgLoadBed command (even though including the full path works). Previous local track installation efforts also did not require the full path to the local track--only that it exist in /gbdb/mm9/bbi/. Not a problem report-just FYI. 2. Love the browser--great work! Please help us get our two lost tracks back! Thanks, Tom _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
