From a29649494a7ccb1010ca1fd5d57aa64460e678f5 Mon Sep 17 00:00:00 2001 From: hexylena Date: Wed, 30 Oct 2024 08:02:46 +0000 Subject: [PATCH 01/14] Import FAQs from Google Form --- .../galaxy/importing-data-from-sierra-lims.md | 14 + ...quest-galaxy-tools-on-a-specific-server.md | 16 + faqs/galaxy/why-isnt-my-history-updating.md | 287 ++++++++++++++++++ faqs/gtn/using-answer-key-histories.md | 19 ++ 4 files changed, 336 insertions(+) create mode 100644 faqs/galaxy/importing-data-from-sierra-lims.md create mode 100644 faqs/galaxy/request-galaxy-tools-on-a-specific-server.md create mode 100644 faqs/galaxy/why-isnt-my-history-updating.md create mode 100644 faqs/gtn/using-answer-key-histories.md diff --git a/faqs/galaxy/importing-data-from-sierra-lims.md b/faqs/galaxy/importing-data-from-sierra-lims.md new file mode 100644 index 00000000000000..f000b3519b1005 --- /dev/null +++ b/faqs/galaxy/importing-data-from-sierra-lims.md @@ -0,0 +1,14 @@ +--- +title: Importing data from Sierra LIMS +layout: faq +area: data upload +box_type: tip +google_form_id: 1730224450 +contributors: +- hexhowells +--- +This section will guide you through generating external links to your data stored in the Sierra LIMS system to be downloaded directly into Galaxy. + +1. Go to the [Sierra portal](https://www.bioinformatics.babraham.ac.uk/sierra/sierra.pl) and login to your account. 2. Click on the **Sample ID** of the sample you want to download data from. 3. Click on the **Edit Sample Details** button. 4. At the bottom of the page there will be an input box for creating a link, enter a description for the link in the **Reason for link** section, and click **Create link**. This will reload the page and add a new link to the sample under **Authorised links to this sample**. 6. Go back to the sample page or click on the hyperlink called **link** to take you back. 7. In the **Results** section select the lane you want to access your data from. 8. The bottom of the page, under the **Links** section, will now contain a list of `wget` commands with links for accessing all the files within that sample/lane. + +9. Since this list is for `wget` commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and paste them directly into Galaxy to download the files. diff --git a/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md b/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md new file mode 100644 index 00000000000000..91ea4a07a2e211 --- /dev/null +++ b/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md @@ -0,0 +1,16 @@ +--- +title: Request Galaxy tools on a specific server +layout: faq +area: tools +box_type: tip +google_form_id: 1728577286 +contributors: +- nomadscientist +--- +To request tools that already exist in the [Galaxy toolshed](https://toolshed.g2.bx.psu.edu), but not in your server, please raise an issue at: + +- *Europe - usegalaxy.eu* | https://github.com/usegalaxy-eu/usegalaxy-eu-tools + +- *USA - usegalaxy.org* | https://github.com/galaxyproject/usegalaxy-tools + +- *Australia - usegaalxy.org.au* | https://github.com/usegalaxy-au/usegalaxy-au-tools/tree/master/usegalaxy.org.au diff --git a/faqs/galaxy/why-isnt-my-history-updating.md b/faqs/galaxy/why-isnt-my-history-updating.md new file mode 100644 index 00000000000000..87a550dfdce78a --- /dev/null +++ b/faqs/galaxy/why-isnt-my-history-updating.md @@ -0,0 +1,287 @@ +--- +title: Why isn't my history updating? +layout: faq +area: "(Other -- Write in comments field)" +box_type: tip +google_form_id: 1729851011 +contributors: +- hexylena +--- +Have you ever experienced that you would submit a job but your history wouldn't update? Maybe it doesn't scroll or the datasets stay permanently grey even when you know they should be complete, *until you refresh the webpage*? + +One possible cause of this can be a difference in the clocks of your browser and the server. Check that your clocks match, and if not, reconfigure them! If you are following the Galaxy Admin Training, you will have setup `chrony`. Check that your `chrony` configuration is valid and requesting time from a local pool. + +``` # chronyc -n sources 210 Number of sources = 1 MS Name/IP address + + + + + + + + Stratum Poll Reach LastRx Last sample + + + + + + + + + + + + + + + +=============================================================================== ^? 169.254.169.123 + + + + + + + + + + + + + + 0 + + 7 + + + + 0 + + + + - + + + + +0ns[ + + +0ns] +/- + + + +0ns + +``` + +This command should return some valid sources. THe above shows an example of a time source that isn't working, 0ns is not a realistic office and LastRx is empty. Instead it should look more like:: + +``` # chronyc -n sources 210 Number of sources = 5 MS Name/IP address + + + + + + + + Stratum Poll Reach LastRx Last sample + + + + + + + + + + + + + + + +=============================================================================== ^? 169.254.169.123 + + + + + + + + + + + + + + 0 + + 6 + + + + 0 + + + + - + + + + +0ns[ + + +0ns] +/- + + + +0ns ^? 178.239.19.58 + + + + + + + + + + + + + + + + 0 + + 6 + + + + 0 + + + + - + + + + +0ns[ + + +0ns] +/- + + + +0ns ^? 194.104.0.153 + + + + + + + + + + + + + + + + 2 + + 6 + + + + 1 + + + + 0 + + +138us[ +138us] +/- + + 30ms ^? 45.138.55.61 + + + + + + + + + + + + + + + + + +1 + + 6 + + + + 1 + + + + 1 + + -103us[ -103us] +/- 3158us ^? 178.239.19.57 + + + + + + + + + + + + + + + + 2 + + 6 + + + + 1 + + + + 1 + + -301us[ -301us] +/- 3240us ``` + +Here we see a number of sources, with more plausible offsets and non-empty LastRx. + +If your time was misconfigured, you might now see something like: + +``` # chronyc -n tracking Reference ID + + + +: B950F724 (185.80.247.36) Stratum + + + + + + + + : 2 Ref time (UTC) + +: Tue Oct 22 09:44:29 2024 System time + + + + : 929.234680176 seconds slow of NTP time ``` + +as chrony slowly adjusts the system clock to match NTP time. + diff --git a/faqs/gtn/using-answer-key-histories.md b/faqs/gtn/using-answer-key-histories.md new file mode 100644 index 00000000000000..23f2f938bc6b22 --- /dev/null +++ b/faqs/gtn/using-answer-key-histories.md @@ -0,0 +1,19 @@ +--- +title: Using answer key histories +layout: faq +area: learners +box_type: tip +google_form_id: 1728648609 +contributors: +- nomadscientist +--- +If you are struggling with a tutorial and you can't figure out why, you can use the answer history (if it's available) which is linked at the top of the tutorial. + +1. Select the *Answer history* and choose the appropriate link from the resulting drop-down menu. + +2. Import the history (If you aren't sure how, [go to the Import History FAQ]({% link faqs/galaxy/histories_import.md %})) 3. Select *View Here* or otherwise navigate to the imported history. 4. Find the dataset that was not outputting for you. You might be able to sport errors from looking at this dataset - such as, you may see that a different tool version was used, or different parameters were run, or different inputs were used. You may find that the input dataset itself is different, and perhaps something has gone wrong earlier in the tutorial for you. + + If you can't find what has gone wrong, you can then: 5. [Ask for help] ({% link faqs/gtn/instructors_getting_help.md %}). + +6. [Copy the necessary datasets over from the answer history into your history]({% link faqs/galaxy/histories_copy_dataset.md %}) so that you can continue your analysis from wherever you got stuck! + From 477ba6b4214f7df2ef7ef8cde8ddc0ac4e37ee22 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 09:09:23 +0100 Subject: [PATCH 02/14] fix formatting of admin faq --- .../faqs}/why-isnt-my-history-updating.md | 287 ++---------------- 1 file changed, 25 insertions(+), 262 deletions(-) rename {faqs/galaxy => topics/admin/faqs}/why-isnt-my-history-updating.md (53%) diff --git a/faqs/galaxy/why-isnt-my-history-updating.md b/topics/admin/faqs/why-isnt-my-history-updating.md similarity index 53% rename from faqs/galaxy/why-isnt-my-history-updating.md rename to topics/admin/faqs/why-isnt-my-history-updating.md index 87a550dfdce78a..89367ac7fad012 100644 --- a/faqs/galaxy/why-isnt-my-history-updating.md +++ b/topics/admin/faqs/why-isnt-my-history-updating.md @@ -1,7 +1,7 @@ --- title: Why isn't my history updating? layout: faq -area: "(Other -- Write in comments field)" +area: debugging box_type: tip google_form_id: 1729851011 contributors: @@ -11,277 +11,40 @@ Have you ever experienced that you would submit a job but your history wouldn't One possible cause of this can be a difference in the clocks of your browser and the server. Check that your clocks match, and if not, reconfigure them! If you are following the Galaxy Admin Training, you will have setup `chrony`. Check that your `chrony` configuration is valid and requesting time from a local pool. -``` # chronyc -n sources 210 Number of sources = 1 MS Name/IP address - - - - - - - Stratum Poll Reach LastRx Last sample - - - - - - - - - - - - - - - -=============================================================================== ^? 169.254.169.123 - - - - - - - - - - - - - - 0 - - 7 - - - - 0 - - - - - - - - - +0ns[ - - +0ns] +/- - - - -0ns +``` +# chronyc -n sources +210 Number of sources = 1 +MS Name/IP address Stratum Poll Reach LastRx Last sample +=============================================================================== +^? 169.254.169.123 0 7 0 - +0ns[ +0ns] +/- 0ns ``` This command should return some valid sources. THe above shows an example of a time source that isn't working, 0ns is not a realistic office and LastRx is empty. Instead it should look more like:: -``` # chronyc -n sources 210 Number of sources = 5 MS Name/IP address - - - - - - - - Stratum Poll Reach LastRx Last sample - - - - - - - - - - - - - - - -=============================================================================== ^? 169.254.169.123 - - - - - - - - - - - - - - 0 - - 6 - - - - 0 - - - - - - - - - +0ns[ - - +0ns] +/- - - - -0ns ^? 178.239.19.58 - - - - - - - - - - - - - - - - 0 - - 6 - - - - 0 - - - - - - - - - +0ns[ - - +0ns] +/- - - - -0ns ^? 194.104.0.153 - - - - - - - - - - - - - - - - 2 - - 6 - - - - 1 - - - - 0 - - +138us[ +138us] +/- - - 30ms ^? 45.138.55.61 - - - - - - - - - - - - - - - - - -1 - - 6 - - - - 1 - - - - 1 - - -103us[ -103us] +/- 3158us ^? 178.239.19.57 - - - - - - - - - - - - - - - - 2 - - 6 - - - - 1 - - - - 1 - - -301us[ -301us] +/- 3240us ``` +``` +# chronyc -n sources +210 Number of sources = 5 +MS Name/IP address Stratum Poll Reach LastRx Last sample +=============================================================================== +^? 169.254.169.123 0 6 0 - +0ns[ +0ns] +/- 0ns +^? 178.239.19.58 0 6 0 - +0ns[ +0ns] +/- 0ns +^? 194.104.0.153 2 6 1 0 +138us[ +138us] +/- 30ms +^? 45.138.55.61 1 6 1 1 -103us[ -103us] +/- 3158us +^? 178.239.19.57 2 6 1 1 -301us[ -301us] +/- 3240us +``` Here we see a number of sources, with more plausible offsets and non-empty LastRx. If your time was misconfigured, you might now see something like: -``` # chronyc -n tracking Reference ID - - - -: B950F724 (185.80.247.36) Stratum - - - - - - - - : 2 Ref time (UTC) - -: Tue Oct 22 09:44:29 2024 System time - - - - : 929.234680176 seconds slow of NTP time ``` +``` +# chronyc -n tracking +Reference ID : B950F724 (185.80.247.36) +Stratum : 2 +Ref time (UTC) : Tue Oct 22 09:44:29 2024 +System time : 929.234680176 seconds slow of NTP time +``` as chrony slowly adjusts the system clock to match NTP time. - From 5170e250598f23d8cb71e56cb42e77c6f3cbd83e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 09:17:47 +0100 Subject: [PATCH 03/14] Smarter FAQ importing --- bin/google-form-faq.rb | 37 +++++++++++++++++++++++++++++++++++-- 1 file changed, 35 insertions(+), 2 deletions(-) diff --git a/bin/google-form-faq.rb b/bin/google-form-faq.rb index 828cc73535884b..93914b14de1c85 100644 --- a/bin/google-form-faq.rb +++ b/bin/google-form-faq.rb @@ -11,6 +11,33 @@ url = 'https://docs.google.com/spreadsheets/d/1RFF3G9_bP8EpfACBk8lnF-Ib43ZGGAMm3ewPwW7eFT0/export?format=tsv' data = `curl -sL "#{url}"` +# We have the problem of renamed FAQs, these will be stored somewhere other +# than the auto-generated name. +# +# We need to eliminate that duplication and ensure we don't overwrite an existing one. +# +# So we need to discover all existing FAQs and their google form IDs. + +def self.discover_faqs + paths = [] + paths += Dir.glob('faqs/**/*.md') + paths += Dir.glob('topics/**/faqs/*.md') + paths += Dir.glob('topics/**/faqs/*.md') + + # Reject symlinks + paths.reject { |path| File.symlink?(path) } +end + +faqs = discover_faqs.map do |path| + metadata = safe_load_yaml(path) + if metadata.is_a?(String) + next + end + + [metadata['google_form_id'], path] +end.reject{|x, y| x.nil?}.to_h + +# The google form data. data = CSV.parse(data, col_sep: "\t", headers: true) count = 0 @@ -20,6 +47,12 @@ post_date = DateTime.strptime(row['Timestamp'], '%d/%m/%Y %H:%M:%S') filename = "faqs/#{row['This FAQ Concerns'].downcase}/#{row['Title'].downcase.gsub(/[^a-z0-9\s-]/i, '').gsub(/\s+/, ' ').gsub(/ /, '-')}.md" + google_form_id = post_date.to_time.to_i + if faqs.include?(google_form_id) + STDERR.puts "Already imported as #{faqs[google_form_id]}" + next + end + # Skip some testing posts if (row['Title'] == 'TESTING') STDERR.puts "Skipping #{filename} as it is a test post" @@ -29,11 +62,11 @@ # Don't overwrite existing posts if File.exist?(filename) other_file = safe_load_yaml(filename) - if other_file['google_form_id'] == post_date.to_time.to_i + if other_file['google_form_id'] == google_form_id STDERR.puts "Skipping #{filename} as it already exists" next else - filename = filename.gsub('.md', "-#{post_date.to_time.to_i}.md") + filename = filename.gsub('.md', "-#{google_form_id}.md") end end From 9c609491218b8f391a5d3803f68083019cd9d57f Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 09:32:28 +0100 Subject: [PATCH 04/14] add faq for admin/containers --- .../admin/faqs/galaxy-jobs-in-containers.md | 123 ++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 topics/admin/faqs/galaxy-jobs-in-containers.md diff --git a/topics/admin/faqs/galaxy-jobs-in-containers.md b/topics/admin/faqs/galaxy-jobs-in-containers.md new file mode 100644 index 00000000000000..2a987fc4f723fe --- /dev/null +++ b/topics/admin/faqs/galaxy-jobs-in-containers.md @@ -0,0 +1,123 @@ +--- +title: How can I get my container requiring jobs to run in a container? +area: galaxy +box_type: tip +layout: faq +contributors: [hexylena] +--- + +Some tools will only run in a container, i.e. they have a container defined in the 'requirements' section of the tool's XML file. +Galaxy will not refuse to run these tools if the container isn't available or if Galaxy isn't configured use containers. Instead it'll run in the host system and likely fail. + +## Job Configuration + +You can resolve this by configuring your job conf to have destinations that support containers (or even require them.): + +The destination must have `docker_enabled` (Or `singularity_enabled`), and you can consider adding `require_container` to make sure the job will fail if the container isn't available. The `docker_volumes` string will allow you to control which volumes are attached to that container; + +In TPV this would look like: + +```yaml + docker: + inherits: slurm + scheduling: + require: + - docker + params: + docker_enabled: true + require_container: true + + singularity: + inherits: slurm + scheduling: + require: + - singularity + params: + singularity_enabled: true + + podman: + inherits: slurm + scheduling: + require: + - podman + params: + docker_enabled: true + require_container: true + docker_volumes: "$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:z,$default_file_path:z" + docker_sudo: false + docker_cmd: /usr/bin/podman + docker_run_extra_arguments: "--userns=keep-id" +``` + +Or in XML: + +```xml + + true + true + + + + true + true + false + /usr/bin/podman + --userns=keep-id + + + + + + true + true + +``` + + +Configuring a tool to use this destination would look like: + +```yaml +toolshed.g2.bx.psu.edu/repos/thanhlv/metaphlan4/metaphlan4/4.0.3: + cores: 12 + mem: cores * 8 + params: + singularity_enabled: true +``` + +Or in XML: + +```xml + + + +``` + +## Container Resolvers Configuration + +If you're using the default `container_resolvers_conf.yml` then there is nothing you need to do. Otherwise you may want to ensure that you have items in there such as `explicit` and `explicit_singularity` among others. See the [galaxy documentation](https://docs.galaxyproject.org/en/master/admin/container_resolvers.html) on the topic. + +## Testing + +Here is an example of a tool that requires a container, that you can use to test your container configuration: + +```xml + + + ubuntu:22.04 + + > '$output'; + hostname -f >> '$output'; + echo "" >> '$output'; + cat /etc/os-release >> '$output'; + echo "" >> '$output'; + env | sort >> '$output'; +]]> + + + + + + + +``` From ad455d48fd36b9f6f7a478b6317907be85abbd14 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 10:51:18 +0100 Subject: [PATCH 05/14] potentially fix linting --- faqs/gtn/using-answer-key-histories.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/faqs/gtn/using-answer-key-histories.md b/faqs/gtn/using-answer-key-histories.md index 23f2f938bc6b22..943dcb87a77364 100644 --- a/faqs/gtn/using-answer-key-histories.md +++ b/faqs/gtn/using-answer-key-histories.md @@ -7,6 +7,7 @@ google_form_id: 1728648609 contributors: - nomadscientist --- + If you are struggling with a tutorial and you can't figure out why, you can use the answer history (if it's available) which is linked at the top of the tutorial. 1. Select the *Answer history* and choose the appropriate link from the resulting drop-down menu. @@ -16,4 +17,5 @@ If you are struggling with a tutorial and you can't figure out why, you can use If you can't find what has gone wrong, you can then: 5. [Ask for help] ({% link faqs/gtn/instructors_getting_help.md %}). 6. [Copy the necessary datasets over from the answer history into your history]({% link faqs/galaxy/histories_copy_dataset.md %}) so that you can continue your analysis from wherever you got stuck! + From e53feb488cf5e1cc5129bce42df5722ae0ad9f47 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 10:53:07 +0100 Subject: [PATCH 06/14] remove bad decisions --- .github/workflows/google-form-events.yml | 1 - .github/workflows/google-form-faqs.yml | 1 - .github/workflows/google-form-news.yml | 2 -- .github/workflows/google-form-recordings.yml | 1 - 4 files changed, 5 deletions(-) diff --git a/.github/workflows/google-form-events.yml b/.github/workflows/google-form-events.yml index ce7b423e01e10b..fc3024f6682dde 100644 --- a/.github/workflows/google-form-events.yml +++ b/.github/workflows/google-form-events.yml @@ -48,7 +48,6 @@ jobs: uses: peter-evans/create-pull-request@v3 with: commit-message: Import events from Google Form - branch-suffix: timestamp title: "[Google Form] New Event!" add-paths: events/ body: | diff --git a/.github/workflows/google-form-faqs.yml b/.github/workflows/google-form-faqs.yml index 7256f33e877867..95fb275050860e 100644 --- a/.github/workflows/google-form-faqs.yml +++ b/.github/workflows/google-form-faqs.yml @@ -48,6 +48,5 @@ jobs: uses: peter-evans/create-pull-request@v3 with: commit-message: Import FAQs from Google Form - branch-suffix: timestamp title: "[Google Form] New FAQ!" add-paths: faqs/ diff --git a/.github/workflows/google-form-news.yml b/.github/workflows/google-form-news.yml index 5a07305e3581ff..77bec959d7c8b0 100644 --- a/.github/workflows/google-form-news.yml +++ b/.github/workflows/google-form-news.yml @@ -48,7 +48,6 @@ jobs: uses: peter-evans/create-pull-request@v3 with: commit-message: Import news posts from Google Form - branch-suffix: timestamp title: "[Google Form] New News Post!" add-paths: news/_posts/ @@ -65,7 +64,6 @@ jobs: uses: peter-evans/create-pull-request@v3 with: title: "[Google Form] New Recording Submission!" - branch-suffix: timestamp commit-message: add new recording from Google Form submission add-paths: topics/ committer: "Saskia Hiltemann " diff --git a/.github/workflows/google-form-recordings.yml b/.github/workflows/google-form-recordings.yml index 5db7c4a0be5e60..0e59afbc158959 100644 --- a/.github/workflows/google-form-recordings.yml +++ b/.github/workflows/google-form-recordings.yml @@ -48,7 +48,6 @@ jobs: uses: peter-evans/create-pull-request@v3 with: title: "[Google Form] New Recording Submission!" - branch-suffix: timestamp commit-message: add new recording from Google Form submission add-paths: topics/ committer: "Saskia Hiltemann " From 136f423615d0cd8cdb53a3077d4f3c2dbfc7c950 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 10:54:22 +0100 Subject: [PATCH 07/14] branch name --- .github/workflows/google-form-events.yml | 1 + .github/workflows/google-form-faqs.yml | 1 + .github/workflows/google-form-news.yml | 2 ++ .github/workflows/google-form-recordings.yml | 1 + 4 files changed, 5 insertions(+) diff --git a/.github/workflows/google-form-events.yml b/.github/workflows/google-form-events.yml index fc3024f6682dde..e98b364c1d0a59 100644 --- a/.github/workflows/google-form-events.yml +++ b/.github/workflows/google-form-events.yml @@ -50,5 +50,6 @@ jobs: commit-message: Import events from Google Form title: "[Google Form] New Event!" add-paths: events/ + branch: google-form/event body: | ${{steps.generate.outputs.pr_message}} diff --git a/.github/workflows/google-form-faqs.yml b/.github/workflows/google-form-faqs.yml index 95fb275050860e..34f52f90c4a4df 100644 --- a/.github/workflows/google-form-faqs.yml +++ b/.github/workflows/google-form-faqs.yml @@ -49,4 +49,5 @@ jobs: with: commit-message: Import FAQs from Google Form title: "[Google Form] New FAQ!" + branch: google-form/faq add-paths: faqs/ diff --git a/.github/workflows/google-form-news.yml b/.github/workflows/google-form-news.yml index 77bec959d7c8b0..9e97c43e2b9123 100644 --- a/.github/workflows/google-form-news.yml +++ b/.github/workflows/google-form-news.yml @@ -49,6 +49,7 @@ jobs: with: commit-message: Import news posts from Google Form title: "[Google Form] New News Post!" + branch: google-form/news add-paths: news/_posts/ - name: Update recordings from Google Form @@ -66,6 +67,7 @@ jobs: title: "[Google Form] New Recording Submission!" commit-message: add new recording from Google Form submission add-paths: topics/ + branch: google-form/recordings committer: "Saskia Hiltemann " author: "Saskia Hiltemann " body: | diff --git a/.github/workflows/google-form-recordings.yml b/.github/workflows/google-form-recordings.yml index 0e59afbc158959..b934d44cc226c1 100644 --- a/.github/workflows/google-form-recordings.yml +++ b/.github/workflows/google-form-recordings.yml @@ -52,6 +52,7 @@ jobs: add-paths: topics/ committer: "Saskia Hiltemann " author: "Saskia Hiltemann " + branch: google-form/recordings body: | New recording submitted! From 0fa168d768f9385be3ebde0389a789c2bdc49f0e Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 11:08:37 +0100 Subject: [PATCH 08/14] remove some logging --- _plugins/api.rb | 2 -- 1 file changed, 2 deletions(-) diff --git a/_plugins/api.rb b/_plugins/api.rb index c6fdb5943eda77..263701d4d1df18 100644 --- a/_plugins/api.rb +++ b/_plugins/api.rb @@ -106,7 +106,6 @@ def generateLibrary(site) page2 = PageWithoutAFile.new(site, '', 'api/', 'data-library.yaml') data_libraries = Dir.glob('topics/**/data-library.yaml') data_libraries.map! { |x| YAML.load_file(x) } - pp data_libraries page2.content = JSON.pretty_generate(Gtn::Git.discover) page2.data['layout'] = nil site.pages << page2 @@ -209,7 +208,6 @@ def generate(site) out = site.data[topic].dup out['materials'] = TopicFilter.topic_filter(site, topic).map do |x| q = x.dup - puts q['url'] q['contributors'] = Gtn::Contributors.get_contributors(q).dup.map do |c| mapContributor(site, c) end From eddcb936ec02ea5667617764b27d40cfc6a560b8 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 11:12:44 +0100 Subject: [PATCH 09/14] reorganise metadata --- faqs/gtn/using-answer-key-histories.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/faqs/gtn/using-answer-key-histories.md b/faqs/gtn/using-answer-key-histories.md index 943dcb87a77364..33f4f0d848be18 100644 --- a/faqs/gtn/using-answer-key-histories.md +++ b/faqs/gtn/using-answer-key-histories.md @@ -1,11 +1,10 @@ --- title: Using answer key histories -layout: faq area: learners +layout: faq box_type: tip google_form_id: 1728648609 -contributors: -- nomadscientist +contributors: [nomadscientist] --- If you are struggling with a tutorial and you can't figure out why, you can use the answer history (if it's available) which is linked at the top of the tutorial. From fbeae41f724899dfb9e3f7bb97218d71c579e302 Mon Sep 17 00:00:00 2001 From: Morgan <58524460+hexhowells@users.noreply.github.com> Date: Wed, 30 Oct 2024 10:14:14 +0000 Subject: [PATCH 10/14] Update last instruction --- faqs/galaxy/importing-data-from-sierra-lims.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/faqs/galaxy/importing-data-from-sierra-lims.md b/faqs/galaxy/importing-data-from-sierra-lims.md index f000b3519b1005..0465ae09f0f8bc 100644 --- a/faqs/galaxy/importing-data-from-sierra-lims.md +++ b/faqs/galaxy/importing-data-from-sierra-lims.md @@ -11,4 +11,4 @@ This section will guide you through generating external links to your data store 1. Go to the [Sierra portal](https://www.bioinformatics.babraham.ac.uk/sierra/sierra.pl) and login to your account. 2. Click on the **Sample ID** of the sample you want to download data from. 3. Click on the **Edit Sample Details** button. 4. At the bottom of the page there will be an input box for creating a link, enter a description for the link in the **Reason for link** section, and click **Create link**. This will reload the page and add a new link to the sample under **Authorised links to this sample**. 6. Go back to the sample page or click on the hyperlink called **link** to take you back. 7. In the **Results** section select the lane you want to access your data from. 8. The bottom of the page, under the **Links** section, will now contain a list of `wget` commands with links for accessing all the files within that sample/lane. -9. Since this list is for `wget` commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and paste them directly into Galaxy to download the files. +9. Since this list is for `wget` commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and {% icon galaxy-wf-edit %} **Paste/Fetch Data** them directly into Galaxy to download the files. From bec9b365d318aa6141fbb84c24dfd22ac99db0df Mon Sep 17 00:00:00 2001 From: Morgan <58524460+hexhowells@users.noreply.github.com> Date: Wed, 30 Oct 2024 10:15:38 +0000 Subject: [PATCH 11/14] Fix list formatting --- faqs/galaxy/importing-data-from-sierra-lims.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/faqs/galaxy/importing-data-from-sierra-lims.md b/faqs/galaxy/importing-data-from-sierra-lims.md index 0465ae09f0f8bc..df7b73580bbe1b 100644 --- a/faqs/galaxy/importing-data-from-sierra-lims.md +++ b/faqs/galaxy/importing-data-from-sierra-lims.md @@ -9,6 +9,11 @@ contributors: --- This section will guide you through generating external links to your data stored in the Sierra LIMS system to be downloaded directly into Galaxy. -1. Go to the [Sierra portal](https://www.bioinformatics.babraham.ac.uk/sierra/sierra.pl) and login to your account. 2. Click on the **Sample ID** of the sample you want to download data from. 3. Click on the **Edit Sample Details** button. 4. At the bottom of the page there will be an input box for creating a link, enter a description for the link in the **Reason for link** section, and click **Create link**. This will reload the page and add a new link to the sample under **Authorised links to this sample**. 6. Go back to the sample page or click on the hyperlink called **link** to take you back. 7. In the **Results** section select the lane you want to access your data from. 8. The bottom of the page, under the **Links** section, will now contain a list of `wget` commands with links for accessing all the files within that sample/lane. - -9. Since this list is for `wget` commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and {% icon galaxy-wf-edit %} **Paste/Fetch Data** them directly into Galaxy to download the files. +1. Go to the [Sierra portal](https://www.bioinformatics.babraham.ac.uk/sierra/sierra.pl) and login to your account. +2. Click on the **Sample ID** of the sample you want to download data from. +3. Click on the **Edit Sample Details** button. +4. At the bottom of the page there will be an input box for creating a link, enter a description for the link in the **Reason for link** section, and click **Create link**. This will reload the page and add a new link to the sample under **Authorised links to this sample**. +5. Go back to the sample page or click on the hyperlink called **link** to take you back. +6. In the **Results** section select the lane you want to access your data from. +7. The bottom of the page, under the **Links** section, will now contain a list of `wget` commands with links for accessing all the files within that sample/lane. +8. Since this list is for `wget` commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and {% icon galaxy-wf-edit %} **Paste/Fetch Data** them directly into Galaxy to download the files. From 0147a7ad1ecb46049fe507647d27ef9186658935 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 11:15:51 +0100 Subject: [PATCH 12/14] thanks for the help --- CONTRIBUTORS.yaml | 4 ++++ topics/admin/faqs/galaxy-jobs-in-containers.md | 4 ++-- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTORS.yaml b/CONTRIBUTORS.yaml index ff84d37bb18b08..56beb6993b621d 100644 --- a/CONTRIBUTORS.yaml +++ b/CONTRIBUTORS.yaml @@ -2397,6 +2397,10 @@ TanguyGen: name: Tanguy Genthon joined: 2023-06 +thanhleviet: + name: Thanh Le Viet + joined: 2024-10 + themudo: name: Gonçalo Themudo joined: 2021-10 diff --git a/topics/admin/faqs/galaxy-jobs-in-containers.md b/topics/admin/faqs/galaxy-jobs-in-containers.md index 2a987fc4f723fe..67e8f0c65d2172 100644 --- a/topics/admin/faqs/galaxy-jobs-in-containers.md +++ b/topics/admin/faqs/galaxy-jobs-in-containers.md @@ -3,7 +3,7 @@ title: How can I get my container requiring jobs to run in a container? area: galaxy box_type: tip layout: faq -contributors: [hexylena] +contributors: [hexylena, thanhleviet] --- Some tools will only run in a container, i.e. they have a container defined in the 'requirements' section of the tool's XML file. @@ -15,7 +15,7 @@ You can resolve this by configuring your job conf to have destinations that supp The destination must have `docker_enabled` (Or `singularity_enabled`), and you can consider adding `require_container` to make sure the job will fail if the container isn't available. The `docker_volumes` string will allow you to control which volumes are attached to that container; -In TPV this would look like: +In TPV configuration (provided by @gtn:thanhleviet) this would look like: ```yaml docker: From bebd1222d97d30e04ccf5ce743e0e20617cb52f9 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 11:28:30 +0100 Subject: [PATCH 13/14] reflow --- faqs/galaxy/importing-data-from-sierra-lims.md | 3 +-- faqs/galaxy/request-galaxy-tools-on-a-specific-server.md | 3 +-- topics/admin/faqs/why-isnt-my-history-updating.md | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/faqs/galaxy/importing-data-from-sierra-lims.md b/faqs/galaxy/importing-data-from-sierra-lims.md index df7b73580bbe1b..cdae1552195129 100644 --- a/faqs/galaxy/importing-data-from-sierra-lims.md +++ b/faqs/galaxy/importing-data-from-sierra-lims.md @@ -4,8 +4,7 @@ layout: faq area: data upload box_type: tip google_form_id: 1730224450 -contributors: -- hexhowells +contributors: [hexhowells] --- This section will guide you through generating external links to your data stored in the Sierra LIMS system to be downloaded directly into Galaxy. diff --git a/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md b/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md index 91ea4a07a2e211..913656f76c6462 100644 --- a/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md +++ b/faqs/galaxy/request-galaxy-tools-on-a-specific-server.md @@ -4,8 +4,7 @@ layout: faq area: tools box_type: tip google_form_id: 1728577286 -contributors: -- nomadscientist +contributors: [nomadscientist] --- To request tools that already exist in the [Galaxy toolshed](https://toolshed.g2.bx.psu.edu), but not in your server, please raise an issue at: diff --git a/topics/admin/faqs/why-isnt-my-history-updating.md b/topics/admin/faqs/why-isnt-my-history-updating.md index 89367ac7fad012..5c118f1aec27b1 100644 --- a/topics/admin/faqs/why-isnt-my-history-updating.md +++ b/topics/admin/faqs/why-isnt-my-history-updating.md @@ -4,8 +4,7 @@ layout: faq area: debugging box_type: tip google_form_id: 1729851011 -contributors: -- hexylena +contributors: [hexylena] --- Have you ever experienced that you would submit a job but your history wouldn't update? Maybe it doesn't scroll or the datasets stay permanently grey even when you know they should be complete, *until you refresh the webpage*? From 0dcb2ba2db7e006ff3153e8d1b9813d5d2750233 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 30 Oct 2024 11:37:03 +0100 Subject: [PATCH 14/14] ugh spacing --- faqs/galaxy/importing-data-from-sierra-lims.md | 1 + 1 file changed, 1 insertion(+) diff --git a/faqs/galaxy/importing-data-from-sierra-lims.md b/faqs/galaxy/importing-data-from-sierra-lims.md index cdae1552195129..bb518281f56aee 100644 --- a/faqs/galaxy/importing-data-from-sierra-lims.md +++ b/faqs/galaxy/importing-data-from-sierra-lims.md @@ -6,6 +6,7 @@ box_type: tip google_form_id: 1730224450 contributors: [hexhowells] --- + This section will guide you through generating external links to your data stored in the Sierra LIMS system to be downloaded directly into Galaxy. 1. Go to the [Sierra portal](https://www.bioinformatics.babraham.ac.uk/sierra/sierra.pl) and login to your account.