| add OptionParser.set_home and set_pairs(); add annotation.pasa.prepare() |
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almost 12 years ago
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| use set_cpus() in apps.last/lastz/blastplus; allow write_file to write python script |
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almost 12 years ago
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| move set_image_options() as a class method of apps.base.OptionParser |
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almost 12 years ago
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| add update_tag() method to formats.gff.GffLine |
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almost 12 years ago
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| allow opening multiple gz/bz2 files |
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almost 12 years ago
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| parallelize finding gaps in formats.fasta.gaps(); add utils.progressbar |
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almost 12 years ago
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| add formats.agp.infer() to guess AGP file given scaffolds and chromosome FASTA |
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almost 12 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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almost 12 years ago
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| Use autogen email address for apps.base.notify(); also allow user to specify custom email address; re-ordered some param groups |
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almost 12 years ago
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| add assembly.trinity; add apps.base.glob() to wrap around glob.glob() |
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almost 12 years ago
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| Fix invocation of apps.base.notify() from apps.base.waitpid() |
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almost 12 years ago
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| Set up grid project code validation in apps.base.OptionParser.set_grid_opts() |
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almost 12 years ago
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| Removed `--cwd` parameter from GridProcess(). Other minor changes |
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almost 12 years ago
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| Added `--unmapped` option to apps.bwa.align() and bwasw() which will retain unmapped reads in separate sam/bam output file. Added a few more grid specific options to apps.grid.GridProcess(class); updated all functions making use of GridProcess. Using `bash` instead of `sh` as executable in subprocess.call() and Popen() |
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almost 12 years ago
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| Added push notification capabilites to apps.base.notify(); currently supports `pushover.net` API; expects an ini config file in the user home area containing the necessary api and user tokens |
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almost 12 years ago
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| Use socket.getfqdn() instead of `dnsdomainname` to get the domain name of current server in apps.base.notify(). Allow sending new process to grid in apps.base.waitpid() |
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almost 12 years ago
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| Added apps.base.waitpid() which waits for a PID to complete and then performs a desired action (notify/execute new process). Added apps.base.notify() which allows sending email to the current user (push notification to be implemented in the future) |
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almost 12 years ago
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| Added in new regexps to annotation.ahrd.fix() to help cleanup some invalid names from Jeff's autonaming pipeline. Minor fix to regexp used in utils.sybase.query() |
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almost 12 years ago
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| Minor fix to formats.base.group() |
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almost 12 years ago
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| add utils.ez_setup; select a list of downloaders (wget, curl, urlopen, etc.) |
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almost 12 years ago
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| Raise AssertionError if runfile and commands list file have the same filename in apps.grid.array(). Autodetect query type in utils.sybase.query() |
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almost 12 years ago
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| Update apps.base.set_grid_opts() to allow specifying task concurrency and output directory. Update apps.grid.GridProcess build() and start() to use the `outdir` from the grid_opts. Fix apps.grid.array() to write out a shell script with the same prefix of the `commands.list` file instead of `array.sh` |
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almost 12 years ago
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| add option --first in assembly.automaton.prepare() |
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almost 12 years ago
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| change assembly.automaton.jira() to prepare() |
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almost 12 years ago
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| add formats.fastq.readlen() to determine max_rd_len |
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almost 12 years ago
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| add --ploidy and --cpus in assembly.allpaths.prepare() |
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almost 12 years ago
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| add assembly.automaton.allpaths() and remove previous allpaths() to allpathsX() |
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almost 12 years ago
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| add assembly.automaton.jira() to extract sequences from JIRA report and automatically assigns to subdir - useful for running many assemblies, e.g. BAC-by-BAC projects |
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almost 12 years ago
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| Minor fix to utils.sybase.query() |
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almost 12 years ago
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| Add in a commit() fn to utils.sybase; add a `--dryrun` option to just display the queries to be executed |
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almost 12 years ago
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