Jun Aruga junaruga
junaruga
/ mitohifi_with_example_data_reads_file.log
Created
October 18, 2022 12:45
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| $ pwd | |
| /home/jaruga/tmp/mitohifi | |
| $ ls -lh exampleFiles | |
| total 39M | |
| -rw-r--r--. 1 jaruga jaruga 1 Oct 11 17:17 .gitkeep | |
| -rw-r--r--. 1 jaruga jaruga 15M Oct 11 17:17 ilDeiPorc1.reads.fa | |
| -rw-r--r--. 1 jaruga jaruga 16K Oct 11 17:17 MW539688.1.fasta | |
| -rw-r--r--. 1 jaruga jaruga 33K Oct 11 17:17 MW539688.1.gb | |
| -rw-r--r--. 1 jaruga jaruga 16K Oct 11 17:17 NC_016067.1.fasta |
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| #!/bin/bash | |
| set -eu | |
| rpm -q redhat-rpm-config | |
| var_names=" | |
| _general_options | |
| __global_compiler_flags | |
| optflags |
junaruga
/ dockstore_tool_launch_with_docker_fedora.log
Created
September 6, 2022 17:54
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| $ make run 2>&1 | tee make_run.log | |
| dockstore tool launch \ | |
| --local-entry "bio-diversity-genomics-garg.wdl" \ | |
| --json "bio-diversity-genomics-garg.inputs.json" | |
| Created temporary working directory at '/tmp/1662486643407-0' | |
| Using local file 'bio-diversity-genomics-garg.wdl' as primary descriptor | |
| Creating directories for run of Dockstore launcher in current working directory: /home/jaruga/git/GargGroup/BioDivGenomics | |
| Provisioning your input files to your local machine | |
| Downloading: BioDivGenomics.input_file from hifi_input.fastq to: /home/jaruga/git/GargGroup/BioDivGenomics/cromwell-input/fe1365e5-3a5b-4166-be1d-087386294496/hifi_input.fastq | |
| Calling out to Cromwell to run your workflow |
junaruga
/ dockstore_tool_launch_with_container_podman.log
Created
September 6, 2022 16:29
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| $ cat /etc/fedora-release | |
| Fedora release 36 (Thirty Six) | |
| $ which podman | |
| /bin/podman | |
| $ which docker | |
| ~/.local/bin/docker | |
| $ ls -l ~/.local/bin/docker |
junaruga
/ FASTK-Dockerfile
Created
September 5, 2022 21:50
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| FROM docker.io/ubuntu:20.04 | |
| ENV FASTK_COMMIT=f18a4e6d2207539f7b84461daebc54530a9559b0 | |
| ENV FASTK_DEST_DIR=/usr/local/bin/ | |
| # Install dependencies. | |
| RUN apt update | |
| RUN apt install -y \ | |
| gcc \ | |
| git \ |
junaruga
/ cromwell_sbt_assembly_54fed3e17.log
Created
September 5, 2022 15:51
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| $ java --version | |
| openjdk 17.0.4 2022-07-19 | |
| OpenJDK Runtime Environment (Red_Hat-17.0.4.0.8-1.fc36) (build 17.0.4+8) | |
| OpenJDK 64-Bit Server VM (Red_Hat-17.0.4.0.8-1.fc36) (build 17.0.4+8, mixed mode, sharing) | |
| $ scala --version | |
| Scala code runner version 2.13.8 -- Copyright 2002-2021, LAMP/EPFL and Lightbend, Inc. | |
| $ sbt --version | |
| WARNING: A terminally deprecated method in java.lang.System has been called |
junaruga
/ framework_polls.txt
Last active
December 19, 2021 01:02
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| For the announce https://community.frame.work/t/now-available-for-pre-order-in-uk-germany-and-france/12359, while I appreciate the consideration to decide the countries based on numbers on the region page. I, who already have the Framework Laptop, didn't register it because I was afraid the selection changes other functionalities such as language experience on the website as I liked English. So, I am curious about this poll on this forum. There are 2 polls: region and country. | |
| If you don't know which region your country will belong to, you can check the following country list. I added the region too. The names of the region and country are by dictionary order and including every countries including micro countries based on the wiki page. To use browswer search, you can press Ctrl (Windows/Linux) or Apple key (Mac) + F 2 times to avoid the search is highjacked by Discourse. And [here](https://meta.discourse.org/t/how-to-create-polls/77548) is Discourse poll building manual. | |
| Please note only people who alread |
junaruga
/ framework_countries.txt
Created
December 18, 2021 23:52
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| 1: Abkhazia, Asia | |
| 2: Afghanistan, Asia | |
| 3: Albania, Europe | |
| 4: Algeria, Africa | |
| 5: American Samoa (United States), Oceania | |
| 6: Andorra, Europe | |
| 7: Angola, Africa | |
| 8: Anguilla (United Kingdom), Americas | |
| 9: Antigua and Barbuda, Americas | |
| 10: Argentina, Americas |
junaruga
/ bundler_cve_f35_ruby_2.6_runtest_dep_api_raise_error.log
Created
December 8, 2021 13:40
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| [mockbuild@0838dc6f5d5545e88ac9166d5017e88c cve-2020-36327]$ ./runtest.sh | |
| * Arguments | |
| * SERVER: geminabox | |
| * RUBYOPT: | |
| * TEST_SILENT: true | |
| * TEST_GEM_VERBOSE: | |
| * TEST_BUNDLE: bundle | |
| * TEST_BUNDLE_DEBUG: | |
| * TEST_BUNDLE_VERBOSE: | |
| * TEST_BUNDLE_INSTALL_INDEX: |
junaruga
/ fedora-ruby-2.6.9-bundler.log
Created
December 8, 2021 12:59
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| + make test-bundler V=1 'RSPECOPTS=--format d' BUNDLER_SPECS=bundler/definition_dep_confusion_spec.rb | |
| # rm -f revision.h | |
| # exit > revision.h || exit > revision.h | |
| ./miniruby -I./lib -I. -I.ext/common ./tool/runruby.rb --extout=.ext -- --disable-gems -C "." bin/gem install --no-document \ | |
| --install-dir .bundle --conservative "rspec:~> 3.5" | |
| Successfully installed rspec-support-3.10.3 | |
| Successfully installed rspec-core-3.10.1 | |
| Successfully installed diff-lcs-1.4.4 | |
| Successfully installed rspec-expectations-3.10.1 | |
| Successfully installed rspec-mocks-3.10.2 |