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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/denis-yuen/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.
Denis Yuen denis-yuen @OICR_news Canada https://orcid.org/0000-0002-6130-1021 OICR Bioinformatics Software Developer

DataBiosphere/topmed-workflows 10

a place for topmed workflows

common-workflow-lab/cwljava 9

Java SDK for CWL

denis-yuen/dockstore-whalesay-wdl-only 2

Sample dockstore whalesay repo for testing

acabunoc/TOT 1

Tips on the Toilet/TV/Twitter

denis-yuen/ampa-nf 0

Fast automated prediction of protein antimicrobial regions

denis-yuen/apigateway 0

AWS in Action: API Gateway

denis-yuen/app-support-prototype 0

A place to explore how we might support "apps" in Dockstore. These are long-running, interactive web services rather than batch workflows.

denis-yuen/arranger 0

🚧 Data Portal Generation

denis-yuen/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273 0

RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.

delete branch dockstore/dockstore

delete branch : feature/postgres_ram_disk

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Denis Yuen

commit sha 345aa713ddc9f901fad3ab7f08cca43871150d74

try older jdbc driver

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Denis Yuen

commit sha f7d384891c618feb0c9dd9729f9106a3190bfce9

newer driver?

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create barnchdockstore/dockstore

branch : feature/what_about_jdbc_driver

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pull request commentdockstore/dockstore

test postgres newer postgres 11 as well

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 357.133 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.532 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.917 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.726 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 28.022 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 32.592 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 34.383 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 20.936 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.647 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 33.66 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.127 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.509 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.188 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.752 s
[INFO] Running io.dockstore.webservice.ServiceIT

11.9

denis-yuen

comment created time in 5 hours

pull request commentdockstore/dockstore

Feature/postgres ram disk

no real boost compared to non-ramdisk, cancelling

denis-yuen

comment created time in 5 hours

PR closed dockstore/dockstore

Feature/postgres ram disk

was curious about https://circleci.com/blog/the-issue-of-speed-and-determinism-in-ci/ and https://circleci.com/docs/2.0/databases/#optimizing-postgres-images

+2 -2

2 comments

2 changed files

denis-yuen

pr closed time in 5 hours

push eventdockstore/dockstore

Denis Yuen

commit sha 0b53386c8c4e5bdb558c94836fff4daa98bd7066

11.9

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Pull request review commentdockstore/dockstore

Revert "Feature/postgres update (#4303)"

         <swagger-annotations-version>1.6.0</swagger-annotations-version>         <openapi-annotations-version>2.1.7</openapi-annotations-version>         <!-- Used for liquibase maven plugin. Somehow use version from bom-internal instead -->-        <postgresql.version>42.2.21</postgresql.version>+        <postgresql.version>42.2.19</postgresql.version>

this is just a git revert

denis-yuen

comment created time in 5 hours

PullRequestReviewEvent

pull request commentdockstore/dockstore

test postgres newer postgres 11 as well

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 348.652 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.94 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.25 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.295 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.455 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.863 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 33.477 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 20.31 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.345 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 33.566 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.948 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.268 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.207 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.734 s

11.10 sigh

denis-yuen

comment created time in 6 hours

PR opened dockstore/dockstore

Feature/postgres ram disk

was curious about https://circleci.com/blog/the-issue-of-speed-and-determinism-in-ci/ and https://circleci.com/docs/2.0/databases/#optimizing-postgres-images

+2 -2

0 comment

2 changed files

pr created time in 6 hours

create barnchdockstore/dockstore

branch : feature/postgres_ram_disk

created branch time in 6 hours

pull request commentdockstore/dockstore

Revert "Feature/postgres update (#4303)"

for the record with 11.8

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 177.463 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 16.279 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 10.179 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 11.818 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 12.389 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 15.838 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.608 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 8.477 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 15.373 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.675 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 10.514 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 7.873 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 8.846 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 9.435 s
denis-yuen

comment created time in 6 hours

pull request commentdockstore/dockstore

test postgres 12.7 out for some binary search action

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 885.169 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 28.049 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.924 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 63.284 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 69.913 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 171.052 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 109.252 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.693 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 123.056 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 77.394 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 43.372 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 27.933 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 34.45 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 72.553 s

nope, 12.0 is slow too

denis-yuen

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push eventdockstore/dockstore

Denis Yuen

commit sha 4fccd93c46db8d6a644ae93eca34aab112491f44

match rds

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issue commentdockstore/dockstore

Tooltester execution logs not visible

think this fix is still chilling in https://github.com/dockstore/dockstore/tree/hotfix/1.11.6 so it won't be in dev or prod

Richard-Hansen

comment created time in 7 hours

pull request commentdockstore/dockstore

test postgres newer postgres 11 as well

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 374.108 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.433 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.764 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.058 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 27.407 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 31.867 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 35.897 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.589 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 32.491 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 36.593 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.647 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.476 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.993 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.156 s
[INFO] Running io.dockstore.webservice.ServiceIT

Weird, better than develop but worse than 1.11 I hope we're not dealing with two issues

denis-yuen

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Denis Yuen

commit sha f99a138e7c8d077ec348b22e978a1739de5c141d

What about the first 12 release?

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pull request commentdockstore/dockstore

test postgres 12.7 out for some binary search action

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 846.903 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.859 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.65 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 61.915 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 69.005 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 128.18 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 89.227 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.132 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 129.888 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 86.305 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 48.153 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.555 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 36.618 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 78.215 s

No good

denis-yuen

comment created time in 8 hours

pull request commentdockstore/dockstore

Revert "Feature/postgres update (#4303)"

note to self, need to update https://github.com/dockstore/dockstore-deploy/blob/develop/database.yml.template#L425

denis-yuen

comment created time in 9 hours

created tagdenis-yuen/hello-dockstore-workflow

tag1.3.6

test repo for CWL and WDL workflows

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release denis-yuen/hello-dockstore-workflow

1.3.6

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Denis Yuen

commit sha 79664f415512d28273994beb2c5d84acde69f43c

Update .dockstore.yml

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Denis Yuen

commit sha db15223af216d10633e6fbd08000080d8b60ffde

Switch to caffeine (#4386) * Switch to caffeine * Reformat * More guava removal

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delete branch dockstore/dockstore

delete branch : feature/reduce_guava

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PR merged dockstore/dockstore

Switch to caffeine

Working on https://ucsc-cgl.atlassian.net/browse/SEAB-598

Despite https://github.com/dropwizard/dropwizard/pull/2400 could not do a clean removal of Guava since it is still a hardcoded dependency of dropwizard-jackson https://github.com/dropwizard/dropwizard/issues/3652

+18 -19

8 comments

5 changed files

denis-yuen

pr closed time in 9 hours

PR opened dockstore/dockstore

test postgres newer postgres 11 as well

this is newer than what aws rds is running, companion to https://github.com/dockstore/dockstore/pull/4388

+2 -2

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Denis Yuen

commit sha 2d46694f17e3e225fed9410fe7a490e2ac19b018

they have a newer 11 as well

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branch : feature/what_about_newer_11

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