Ecosyste.ms: Issues

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GitHub / fstrozzi/bioruby-pipengine issues and pull requests

#43 - Fixing missing comma

Pull Request - State: closed - Opened by arfon over 7 years ago

#42 - Idiotproofing

Issue - State: closed - Opened by yannickwurm over 7 years ago

#41 - Specific dependencies?

Issue - State: closed - Opened by yannickwurm over 7 years ago - 1 comment

#40 - Example data for testing?

Issue - State: closed - Opened by yannickwurm over 7 years ago

#39 - re-add 'pipengine jobs' support

Issue - State: closed - Opened by bunop almost 9 years ago - 1 comment

#38 - Introduce the <sample_group> place holder.

Pull Request - State: open - Opened by rjpbonnal almost 9 years ago - 1 comment

#37 - erb was missing

Pull Request - State: closed - Opened by rjpbonnal about 9 years ago

#36 - New option to process automatically all the groups.

Pull Request - State: closed - Opened by rjpbonnal over 9 years ago - 1 comment

#35 - Generate scripts even if Torque/PBS is not specified

Issue - State: closed - Opened by george-githinji over 9 years ago - 3 comments

#34 - single step 'local resources' directly from pipengine command line

Issue - State: closed - Opened by rgiannico almost 10 years ago - 1 comment

#33 - Step dependencies (other step files)

Issue - State: closed - Opened by rgiannico almost 10 years ago - 3 comments

#32 - check if all resources has been provided

Issue - State: closed - Opened by rgiannico almost 10 years ago - 2 comments

#31 - Groups processing (Cuffdiff, Cuffnorm)

Issue - State: closed - Opened by arrigonialberto86 almost 10 years ago - 1 comment

#30 - Process groups altogether

Issue - State: closed - Opened by arrigonialberto86 almost 10 years ago - 1 comment

#29 - Improved logs

Pull Request - State: closed - Opened by rjpbonnal almost 10 years ago

#28 - log and dependencies

Pull Request - State: closed - Opened by rjpbonnal almost 10 years ago

#27 - close issue #26

Pull Request - State: closed - Opened by rjpbonnal over 10 years ago

#26 - --pbs-queue is not the actual parameters which is queue

Issue - State: closed - Opened by rjpbonnal over 10 years ago

#25 - Using Environment modules with pipengine

Issue - State: closed - Opened by arrigonialberto86 over 10 years ago

#24 - Master script for pipeline exec

Issue - State: open - Opened by arrigonialberto86 over 10 years ago

#23 - Add option to enable PBS sending email to the user

Issue - State: closed - Opened by fstrozzi about 11 years ago
Labels: enhancement

#22 - Add a --batch option to avoid opening an SSH connection to the PBS Server or Masternode for every job launched

Issue - State: closed - Opened by fstrozzi over 11 years ago - 2 comments
Labels: bug, enhancement

#21 - Change Job Name to use a combination of Sample Name and Step Name

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#20 - Add logging feature to save information such as the pipeline used, the steps etc.

Issue - State: open - Opened by fstrozzi over 11 years ago
Labels: enhancement

#19 - Fix create samples method to avoid picking up files as sample directories

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: bug

#18 - Add the support for organizing samples into groups

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#17 - Create a config file where scheduler type and pipelines folder are specified

Issue - State: open - Opened by fstrozzi over 11 years ago
Labels: maybe someday

#15 - Add support for Qdel through TORQUE RM

Issue - State: closed - Opened by fstrozzi over 11 years ago

#14 - Implement subcommands for pipengine command line to better handle pbs stats

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#13 - Add check for .torque_rm file

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#12 - Check if previous step directory exists when there are dependencies

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#11 - Print the job ID after submit

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#10 - Implement qstat report from command line using Torque RM

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#9 - Generate a single samples.yml for all the projects under the same run folder

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#8 - Change UUID generation

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#7 - DRMAA support to use different queue system

Issue - State: closed - Opened by rjpbonnal over 11 years ago

#6 - Generate sample configuration by project or run directory

Issue - State: closed - Opened by rjpbonnal over 11 years ago
Labels: enhancement

#5 - Refactor the code to shift to a more OO style

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: refactor

#4 - Change the multi-step behaviour

Issue - State: closed - Opened by fstrozzi over 11 years ago
Labels: enhancement

#3 - Adding a 'description' field for the steps in the pipeline yaml

Issue - State: closed - Opened by fstrozzi almost 12 years ago
Labels: enhancement

#2 - Add command line options to be passed to the PBS/Torque scheduler

Issue - State: closed - Opened by fstrozzi almost 12 years ago
Labels: enhancement

#1 - Add placeholder to specify only the path to a previous step folder

Issue - State: closed - Opened by fstrozzi almost 12 years ago
Labels: enhancement