run_tool.sh V1 Name project-75-RNAseqHumanBrain settings.json V1 Version Control Example: update central repository Server Central Repository for Server project-75-RNAseqHumanBrain Local Repository for project-75-RNAseqHumanBrain Pushes to central repository to synchronize. Chris 24/141 GitLab as a Collaborative Working Environment
V1 settings.json V1 run_tool.sh Name project-75-RNAseqHumanBrain Version Control Example: update local repository Server Central Repository for Server project-75-RNAseqHumanBrain Local Repository for project-75-RNAseqHumanBrain Pulls from central repository to synchronize her local one. Jeny 25/141 GitLab as a Collaborative Working Environment
7 16 run_tool.sh 8 9 10 11 12 13 14 15 17 5 18 settings.json run_tool.sh Name project-75-RNAseqHumanBrain settings.json #!�/bin/bash tool�src�target�-config�settings.json� 1 2 6 4 4 ����"strand_protocol":�"dutp", V1 V1 { ��"ratio":�100, ��"gentrap":�{ ����"expression_measures":�[ ������"fragments_per_gene", ������"cufflinks_strict" ����],���� ����"call_variants":�false, 3 ����"aligner":�"gsnap", ����"gsnap":�{ �������"exe":�"/usr/local/bin/gsnap", �������"npaths":�1, �������"threads":�8 ����} ��} } 1 2 3 Version Control Example: edit again the second file Makes more changes to the con fi guration. Jeny 26/141 GitLab as a Collaborative Working Environment
8 17 V1 9 10 11 12 13 14 15 16 settings.json 6 run_tool.sh Name project-75-RNAseqHumanBrain settings.json #!�/bin/bash tool�src�target�-config�settings.json� 1 2 3 7 5 run_tool.sh ����"aligner":�"gsnap", V2 { ��"ratio":�100, ��"gentrap":�{ ����"expression_measures":�[ ������"fragments_per_gene", ������"cufflinks_strict" ����],���� ����"call_variants":�false, ����"gsnap":�{ 4 �������"exe":�"/usr/local/bin/gsnap", �������"npaths":�1, �������"threads":�8 ����} ��} } 1 2 3 4 Version Control Example: save again the second file to the repository Saves the new version of the con fi guration fi le. Jeny 27/141 GitLab as a Collaborative Working Environment
11 17 8 9 10 V1 12 13 14 15 16 settings.json 6 run_tool.sh Name project-75-RNAseqHumanBrain settings.json #!�/bin/bash tool�src�target�-config�settings.json� 1 2 3 7 5 run_tool.sh ����"aligner":�"gsnap", V2 { ��"ratio":�100, ��"gentrap":�{ ����"expression_measures":�[ ������"fragments_per_gene", ������"cufflinks_strict" ����],���� ����"call_variants":�false, ����"gsnap":�{ 4 �������"exe":�"/usr/local/bin/gsnap", �������"npaths":�1, �������"threads":�8 ����} ��} } 1 2 3 4 Version Control Example: more results Something interesting 1 Both here 0 1 And here The plot is updated. Jeny 28/141 GitLab as a Collaborative Working Environment
run_tool.sh Name V2 V1 settings.json project-75-RNAseqHumanBrain Version Control Example: update central repository again Server Central Repository for Server project-75-RNAseqHumanBrain Local Repository for project-75-RNAseqHumanBrain Pushes to central repository to synchronize. Jeny 29/141 GitLab as a Collaborative Working Environment
project-75-RNAseqHumanBrain Version Control Example: intermediate results project discussion Jeny Look what I can show you before I leave for holidays. Something interesting 1 Chris Thomas Both here That's very nice, but I'll solve it , don't worry. something is missing. 0 1 And here Barbara 30/141 GitLab as a Collaborative Working Environment
run_tool.sh Name V2 V1 settings.json project-75-RNAseqHumanBrain Version Control Example: update local repository again Server Central Repository for Server project-75-RNAseqHumanBrain Local Repository for project-75-RNAseqHumanBrain Pulls from central repository to synchronize his local one. Chris 31/141 GitLab as a Collaborative Working Environment
����],���� 8 ������"fragments_per_gene", ����"expression_measures":�[ ��"gentrap":�{ ��"ratio":�100, { settings.json 12 11 10 9 7 ����],���� 6 5 4 3 2 1 } ��} ����"call_variants":�false ����"strand_protocol":�"dutp", V1 ������"cufflinks_strict" ����"call_variants":�false, ������"fragments_per_gene", 6 16 15 14 13 12 11 10 9 8 7 5 ����"aligner":�"gsnap", 4 3 2 1 } ��} ����} �������"threads":�8 �������"npaths":�1, �������"exe":�"/usr/local/bin/gsnap", ����"gsnap":�{ ������"cufflinks_strict" ����"expression_measures":�[ settings.json ����} 10 9 8 7 6 5 ... settings.json } ��} �������"threads":�8 ... �������"npaths":�1, �������"exe":�"/usr/local/bin/gsnap", ����"gsnap":�{ ����"aligner":�"gsnap", ����"call_variants":�false, ����"call_variants":�false ����"strand_protocol":�"dutp", ����],���� ������"cufflinks_strict" ������"fragments_per_gene", V2 11 ... ��"gentrap":�{ - ��"ratio":�100, { 7�additions�and�2�deletions + + + + + + + - ... 5 16 15 14 13 12 11 10 9 8 7 6 17 Version Control Example: check the differences with an older version vs Finds deleted line. Chris 32/141 GitLab as a Collaborative Working Environment
8 17 V1 9 10 11 12 13 14 15 16 18 6 settings.json run_tool.sh Name project-75-RNAseqHumanBrain settings.json #!�/bin/bash tool�src�target�-config�settings.json� 1 2 3 7 5 run_tool.sh ����"call_variants":�false, V2 { ��"ratio":�100, ��"gentrap":�{ ����"expression_measures":�[ ������"fragments_per_gene", ������"cufflinks_strict" ����],���� ����"strand_protocol":�"dutp", ����"aligner":�"gsnap", 4 ����"gsnap":�{ �������"exe":�"/usr/local/bin/gsnap", �������"npaths":�1, �������"threads":�8 ����} ��} } 1 2 3 4 Version Control Example: make changes Repairs the con fi guration. Chris 33/141 GitLab as a Collaborative Working Environment
12 18 9 10 11 V3 13 14 15 16 17 settings.json 7 run_tool.sh Name project-75-RNAseqHumanBrain settings.json #!�/bin/bash tool�src�target�-config�settings.json� 1 2 3 4 8 6 V1 ����"aligner":�"gsnap", { ��"ratio":�100, ��"gentrap":�{ ����"expression_measures":�[ ������"fragments_per_gene", ������"cufflinks_strict" ����],���� ����"strand_protocol":�"dutp", ����"call_variants":�false, ����"gsnap":�{ 5 �������"exe":�"/usr/local/bin/gsnap", �������"npaths":�1, �������"threads":�8 ����} ��} } 1 2 3 4 run_tool.sh Version Control Example: first results draft Something interesting 0 Both here 0 1 And here Real results. Chris 34/141 GitLab as a Collaborative Working Environment
run_tool.sh Name V3 V1 settings.json project-75-RNAseqHumanBrain Version Control Example: final central repository update Server Central Repository for Server project-75-RNAseqHumanBrain Local Repository for project-75-RNAseqHumanBrain Pushes to central repository to synchronize. Chris 35/141 GitLab as a Collaborative Working Environment
project-75-RNAseqHumanBrain Version Control Example: results discussion meeting Jeny Something interesting 0 Chris Thomas Both here 0 1 And here Barbara 36/141 GitLab as a Collaborative Working Environment
GitLab 37/141 GitLab as a Collaborative Working Environment
GitLab What is GitLab? GitLab is an application to code, test, and deploy code together. It provides Git repository management with: • fine grained access controls; • code reviews; • issue tracking; • activity feeds; • wikis; • continuous integration. — https://about.gitlab.com/about/ 38/141 GitLab as a Collaborative Working Environment
GitLab Overview: without GitLab Server Central Server Repository (Version Database) Local Repository Local Repository Jeny Thomas Local Repository Local Repository Chris Barbara 39/141 GitLab as a Collaborative Working Environment
GitLab Overview: with GitLab I GitLab acts like a wrapper for the server repository: Server - Is is a self-hosted system for Central managing your projects; Server Repository - It adds many features on top of Git. (Version Database) Local Repository Local Repository GitLab Jeny Thomas Local Repository Local Repository Chris Barbara 40/141 GitLab as a Collaborative Working Environment
GitLab Overview: with GitLab II Server Central Server Browser access. Repository (Version Database) GitLab https://git.lumc.nl Local Repository Projects project-49-Biopet project-54-DNAT esting project-75-RNAseqHumanBrain GitLab Jeny Thomas Local Repository Local Repository Chris Barbara 41/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment o-Dos L a i b k e T i W l s Projects Milestones M s e GitLab e u m Groups s s b I e r s 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment o-Dos L a i b k e T i W l s Projects Milestones Equivalent to separate versioned repositories. M s e GitLab e u m Groups s s b I e r s 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment s Wiki T t c o e - D j o o r s P Members Labels Users who have access to the projects. G s e GitLab r o n u o Issues p t s s e l i M 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment Projects s r e b m W e i M k i Groups T o-Dos Users that share access rights and namespaces. Collections of several projects. s I s l GitLab s e u b Milestones e a s L 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment Members P s r p o u j e o c r t G s Issues Wiki A manner through which changes are requested. s M o GitLab i D l e Labels - s o t T o n e s 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment Groups M e m s e b u e s r s s I Projects Milestones Allow issues organization and, optionally, setting a due date. L i k a GitLab i b W e o-Dos l s T 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment s Issues e n G o t r s o e u l p i M s Labels Members Provide an easy way to categorize issues based on descriptive titles. T s o t GitLab c - D e Wiki j o o s r P 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment Milestones s I s l e s b u e a L s Groups T o-Dos See where you should spend your time, where your team members need help, s W r GitLab i e where you need to take some action, k b Projects i m or what you need to keep an eye on. e M 42/141 GitLab as a Collaborative Working Environment
GitLab Collaborative Environment M Labels i l e s s o t o D n - e o T s Wiki Issues Keep your project documentation using the built-in wiki system. s P p r GitLab o u j o Members e r c G t s 42/141 GitLab as a Collaborative Working Environment
GitLab Projects • A GitLab project corresponds to a single Git repository. • Every project has a visibility level: • A way of controling who has read access to that project. • Every project belongs to a single namespace, either a: • User: • The project owner has direct control over the project. • Group: • The group’s user-level permissions will take effect. 43/141 GitLab as a Collaborative Working Environment
GitLab Project visibility levels • Private projects: • The project owner must explicitly grant access to specific users. • Are not listed on the public access directory. • Internal projects: • Can be cloned by any logged in user. • Are listed on the public access directory for logged in users. • Logged in users have Guest permissions on the repository. • Public projects: • Can be cloned without any authentication. • Are listed on the public access directory. • Logged in users have Guest permissions on the repository. 44/141 GitLab as a Collaborative Working Environment
GitLab Users and groups User actions: • Create / import / manage projects. • Create / manage groups. User roles per project/group: • Guest. • Reporter. • Developer. • Master. • Owner. 45/141 GitLab as a Collaborative Working Environment
GitLab Example GitLab Jeny https://git.lumc.nl Welcome to the LUMC GitLab server Chris LUMC GitLab Users Thomas GitLab o ff ers git repository management, code reviews, issue tracking, activity feeds and wikis. This server is free to use for LUMC employees and collaborators. Barbara 46/141 GitLab as a Collaborative Working Environment
GitLab Example: group creation GitLab https://git.lumc.nl New Group Group path https://git.lumc.nl/ CR Description Department of Core Research. Visibility Level Private Internal Public Create group Cancel Creates department group. Thomas 47/141 GitLab as a Collaborative Working Environment
GitLab Example: add users to group GitLab https://git.lumc.nl/groups/CR/group_members Add new user to group Members of group have access to all group projects. People Jeny Chris Search for users by name, username, or email, or invite new ones using their email address. Group Access Developer Access expiration Select access expiration date date Add users to group Adds colleagues to the department group. Thomas 48/141 GitLab as a Collaborative Working Environment
GitLab Example: group access email confirmation Outlook Web App https://mail.lumc.nl/owa/ OutlookWebApp Inbox Access to the CR ... Access to the CR group was granted GitLab-LUMC [gitlab.noreply@git.lumc.nl] T o: Jeny, Chris Inbox You have been granted Developer access to the CR group. - Receive con fi rmation emails. Jeny Chris 49/141 GitLab as a Collaborative Working Environment
GitLab Example: project creation GitLab https://git.lumc.nl/projects/new New project Project path Project name https://git.lumc.nl/ CR project-75-RNAseqHumanBrain Import project from git Repo by URL Git repository URL http://some-non-gitlab.project.location/ Project description Extremely innovative project. Visibility Level Private Internal Not selectable since it is created under a private group. Public Create project Cancel Creates GitLab project for "project-75-RNAseqHumanBrain". Thomas 50/141 GitLab as a Collaborative Working Environment
GitLab Quiz: permissions I Do Jeny and Chris have access to the “project-75- RNAsetqHumanBrain” project? What about Barbara? 51/141 GitLab as a Collaborative Working Environment
GitLab Example: current roles Group Project CR project-75-RNAseqHumanBrain Thomas Owner Owner Jeny Developer Developer Inherited from the group Developer Developer Chris Neither group nor project access for Barbara. Barbara - - 52/141 GitLab as a Collaborative Working Environment
GitLab Example: add users to project GitLab https://git.lumc.nl/RC/project-75-RNAseqHumanBrain/project_members Add new user to project Members of group have access to all group projects. People Barbara Search for users by name, username, or email, or invite new ones using their email address. Project Access Developer Access expiration Select access expiration date date Add users to project Adds Barbara to the project. Thomas 53/141 GitLab as a Collaborative Working Environment
GitLab Quiz: permissions II Does Barbara have access to other group projects now? 54/141 GitLab as a Collaborative Working Environment
GitLab Example: roles updated Group Project CR project-75-RNAseqHumanBrain Thomas Owner Owner Jeny Developer Developer Developer Developer Chris Receives also an email with this information. Barbara - Developer 55/141 GitLab as a Collaborative Working Environment
GitLab Users and groups extras • You can import another project’s users into your own project. • You can request access to a project/group (if enabled). • You can share your project with other groups. • You can manage group/project members roles at any time. 56/141 GitLab as a Collaborative Working Environment
Last�Commit�>�c12a4211�-�1�day�ago History 1�day�ago 1�day�ago V3 v1 settings.json Name run_tool.sh Last�update GitLab Example: view project files on GitLab GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ + Find File Browses the project fi les. Thomas 57/141 GitLab as a Collaborative Working Environment
Last�Commit�>�c12a4211�-�1�day�ago History 1�day�ago 1�day�ago V3 v1 settings.json Name run_tool.sh Last�update GitLab Example: view project files on GitLab GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ + Find File Clicks on a fi le. Thomas 57/141 GitLab as a Collaborative Working Environment
��} ����} ����"strand_protocol":�"dutp", ����"call_variants":�false, ����"aligner":�"gsnap", ����"gsnap":�{ ������"exe":�"/usr/local/bin/gsnap", ������"npaths":�1, ������"threads":�8 9 ������"cufflinks_strict" } 1 2 3 4 5 6 ����], ������"fragments_per_gene", 8 11 c12a4211 17 16 15 14 13 12 10 ����"expression_measures":[ V3 Chris�authored�about�1�day�ago settings.json 314�Bytes { ��"ratio":�100, ��"gentrap":{ 7 GitLab Example: view project files on GitLab GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/blob/master/settings.json Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ settings.json Raw Blame History Permalink Edit Replace Delete Is able to see the fi le contents. Thomas 57/141 GitLab as a Collaborative Working Environment
��} ����} ����"strand_protocol":�"dutp", ����"call_variants":�false, ����"aligner":�"gsnap", ����"gsnap":�{ ������"exe":�"/usr/local/bin/gsnap", ������"npaths":�1, ������"threads":�8 9 ������"cufflinks_strict" } 1 2 3 4 5 6 ����], ������"fragments_per_gene", 8 11 c12a4211 17 16 15 14 13 12 10 ����"expression_measures":[ V3 Chris�authored�about�1�day�ago settings.json 314�Bytes { ��"ratio":�100, ��"gentrap":{ 7 GitLab Example: see file history GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/blob/master/settings.json Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ settings.json Raw Blame History Permalink Edit Replace Delete Clicks the History button. Thomas 58/141 GitLab as a Collaborative Working Environment
4�commits c12a4211 V0 Chris�authored�about�11�days�ago c09c5517 V1 Chris�authored�about�10�days�ago b82a1234 V2 Jeny�authored�about�5�days�ago a53d5341 V3 Chris�authored�about�1�day�ago GitLab Example: see file history GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/commits/master/settings.json Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ settings.json Filter by commit message Clicks the History button. Thomas 58/141 GitLab as a Collaborative Working Environment
4�commits c12a4211 V0 Chris�authored�about�11�days�ago c09c5517 V1 Chris�authored�about�10�days�ago b82a1234 V2 Jeny�authored�about�5�days�ago a53d5341 V3 Chris�authored�about�1�day�ago GitLab Example: see differences GitLab https://git.lumc.nl/CR/project-75-RNAsetqHumanBrain/blob/master/settings.json Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ settings.json Filter by commit message Clicks on the commit message. Thomas 59/141 GitLab as a Collaborative Working Environment
11 9 9 10 + ... ... 5 6 7 8 10 7 11 12 13 14 15 16 ... - - + 8 6 + ����"call_variants":�false Authored�by� Jeny �����about�5�days�ago Showing�1�changed�file�with�7�additions�and�2�deletions + + + ������"fragments_per_gene", ������"cufflinks_strict" ����],���� ����"strand_protocol":�"dutp", ����"call_variants":�false, 5 ����"aligner":�"gsnap", ����"gsnap":�{ �������"exe":�"/usr/local/bin/gsnap", �������"npaths":�1, �������"threads":�8 ����} ��} } settings.json ... + GitLab Example: see differences GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/commit/a53d5341164dfd9cf2515b059ad37356cce6b04d Repository V1 Is able to see the di ff erences. Thomas 59/141 GitLab as a Collaborative Working Environment
Last�Commit�>�c12a4211�-�1�day�ago History 1�day�ago 1�day�ago V3 v1 settings.json Name run_tool.sh Last�update GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ + Find File Browses the project fi les. Thomas 60/141 GitLab as a Collaborative Working Environment
Last�Commit�>�c12a4211�-�1�day�ago History 1�day�ago 1�day�ago V3 v1 settings.json Name run_tool.sh Last�update GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ + Find File Starts the uploading fi le process. Thomas 60/141 GitLab as a Collaborative Working Environment
Name run_tool.sh New�tag New�branch New�directory Upload�file New�file 1�day�ago 1�day�ago Last�update History Last�Commit�>�c12a4211�-�1�day�ago V3 v1 settings.json GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ + Find File Starts the uploading fi le process. Thomas 60/141 GitLab as a Collaborative Working Environment
GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Upload New File Attach a fi le by drag & drop or click to upload Commit message Upload new fi le T arget branch master Upload fi le Cancel Starts the uploading fi le process. Thomas 60/141 GitLab as a Collaborative Working Environment
GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Upload New File Attach a fi le by drag & drop or click to upload awesome_ settings.json Commit message Upload new fi le T arget branch master Upload fi le Cancel Drags the fi le. Thomas 60/141 GitLab as a Collaborative Working Environment
GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Upload New File Attach a fi le by drag & drop or click to upload awesome_ settings.json Commit message Upload new fi le T arget branch master Upload fi le Cancel Changes the commit message. Thomas 60/141 GitLab as a Collaborative Working Environment
GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Upload New File Attach a fi le by drag & drop or click to upload awesome_ settings.json Commit message Upload best settings fi le ever T arget branch master Upload fi le Cancel Changes the commit message. Thomas 60/141 GitLab as a Collaborative Working Environment
GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Upload New File Attach a fi le by drag & drop or click to upload awesome_ settings.json Commit message Upload best settings fi le ever T arget branch master Upload fi le Cancel Presses the Upload fi le button. Thomas 60/141 GitLab as a Collaborative Working Environment
run_tool.sh Name 1�minute�ago Upload�best�settings�file�ever� awesome_settings.json 1�day�ago 1�day�ago Last�update History Last�Commit�>�c34a5133�-�1�minute�ago V3 v1 settings.json GitLab Example: upload existing file GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/tree/master Repository Files Commits Network ... master project-75-RNAseqHumanBrain/ + Find File The new fi le appears in the repository. Thomas 60/141 GitLab as a Collaborative Working Environment
Practical 1 Groups, Projects, and File Handling 61/141 GitLab as a Collaborative Working Environment
Issues Allow you signalize problems and to delegate their solving to people. You can make issues and: • Assign them to people. • Leave them general (unassigned). • Have discussions in them. • File them under milestones (detailed later). 62/141 GitLab as a Collaborative Working Environment
Example: issue creation GitLab https://git.lumc.nl/CR/project-75-RNAsetqHumanBrain/issues/new New Issue Title Simulation is way to slow Description We should fi nd a solution to reduce simulation time asap. Maybe Barbara can help with this? Styling with Markdown and slash commands are supported Assignee Due date Select due date Barbara Milestone Select milestone Submit issue Cancel Creates a general issue and assigns it to Barbara. Thomas 63/141 GitLab as a Collaborative Working Environment
Example: issue assignation email notification Outlook Web App https://mail.lumc.nl/owa/ OutlookWebApp Inbox project-75-RNAse ... project-75-RNAseqHumanBrain | Simulation is way to slow (#1) Access to the pro ... Thomas [gitlab.noreply@git.lumc.nl] T o: Barbara Inbox We should fi nd a solution to reduce simulation time asap. Maybe Barbara can help with this? Assignee: Barbara — View it on GitLab. You're receiving this email because of your account on git.lumc.nl. If you'd like to receive fewer emails, you can unsubscribe from this thread or adjust your noti fi cation settings. Receives email with the new issue created and assigned to her. Barbara 64/141 GitLab as a Collaborative Working Environment
Example: the issue appears as a To do GitLab https://git.lumc.nl/dashboard/todos 1 T o do 1 CR/project-75-RNAseqHumanBrain Thomas assigned you issue #1 · 10 minutes ago Done Simulation is way to slow Logs in to GitLab. The issue appears also as a T o do noti fi cation. Barbara 65/141 GitLab as a Collaborative Working Environment
Example: issue reply GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/issues/1 1 Issue #1 opened about an hour ago by Thomas Simulation is way to slow We should fi nd a solution to reduce simulation time asap. Maybe Barbara can help with this? Running it on shark would be an option. I will give it a try. 12 Styling with Markdown and slash commands are supported Comment Comment & close issue Discard draft Uses the issues discussion option to reply. Barbara 66/141 GitLab as a Collaborative Working Environment
Example: issue reply again GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/issues/1 Issue #1 opened about an hour ago by Thomas Simulation is way to slow We should fi nd a solution to reduce simulation time asap. Maybe Barbara can help with this? Barbara commented 20 minutes ago. Running it on shark would be an option. I will give it a try. Great idea. Good luck with that! Styling with Markdown and slash commands are supported Comment Comment & close issue Discard draft Replies back to Barbara. Email noti fi cation not shown. Thomas 67/141 GitLab as a Collaborative Working Environment
7 #$�-M�barbara@lumc.nl 10 9 8 13 6 5 4 3 2 1 tool�src�target�-ratio�100�-config�settings.json� #$�-m�be 12 #$�-V #$�-j�Y #$�-cwd #$�-l�h_vmem=16g #$�-pe�BWA�16 #$�-N�CR_tool #$�-q�all.q� #$�-S�/bin/bash� #!�/bin/bash 14 run_tool.sh 11 Example: edit file directly on GitLab GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/edit/master/run_tool.sh Edit File Commit message Add shark run con fi guration. Edits the fi le using the GitLab T arget branch master interface. Commit Changes Cancel Barbara 68/141 GitLab as a Collaborative Working Environment
Example: close issue GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/edit/master/run_tool.sh Issue #1 opened about 2 hours ago by Thomas Open Simulation is way to slow We should fi nd a solution to reduce simulation time asap. Maybe Barbara can help with this? Barbara commented 2 hours ago. Running it on shark would be an option. I will give it a try. Thomas commented about 1 hour ago. Great idea. Good luck with that! Please make use of the new script. Utilize qsub to run it on the shark server. `qsub run_tool.sh` You can fi nd more information [here](https://git.lumc.nl/shark/SHARK). Styling with Markdown and slash commands are supported Comment Comment & close issue Discard draft Replies with solution and closes the issue. Email noti fi cation not shown. Barbara 69/141 GitLab as a Collaborative Working Environment
Issues extras • You can reassign an issue. • You can reopen an issue. • You can still make comments in closed issues. • You can upvote/downvote issues or add emojis. • You can categorize issues with labels (detailed later). 70/141 GitLab as a Collaborative Working Environment
Todos A chronological list of things that are waiting for your input. Todos allow you to see where: • You should spend your time. • Your team members need help. • You need to take some action. • You need to keep an eye on. Note that Todos are personal. 71/141 GitLab as a Collaborative Working Environment
Todos triggering A Todo is triggered when: • An issue is assigned to you. • You are @mentioned in an issue. • Be it the description or in a comment. You can also manually add an issue to your Todos list. Note that there is just one Todo per issue. 72/141 GitLab as a Collaborative Working Environment
Todos dismissal Any of the following action to the corresponding issue will mark your Todo as Done: • Changing the assignee. • Changing the milestone. • Adding/removing a label. • Commenting on the issue. You can also manually mark the Todo as done. Todos are only marked as Done if the action is coming from you. 73/141 GitLab as a Collaborative Working Environment
Labels • Categorize and filter issues based on descriptions. • They can have different colors. • Predefined labels are available. • You can prioritize labels. • You can subscribe to be notified when a label gets added to an issue. 74/141 GitLab as a Collaborative Working Environment
Example: create a label GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/labels/new New Label Title simulation Description Anything which is related to simulations. Background color click here for any color picker Choose any color. Or you can choose one of the suggested colors below Create Label Cancel Creates a new label to be assigned to simulation related issues. Barbara 75/141 GitLab as a Collaborative Working Environment
Example: assign label to issue GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/issues/1 Issue #1 opened about 6 hours ago by Thomas Closed T odo Add T odo Simulation is way to slow Assignee Edit We should fi nd a solution to reduce simulation time asap. Maybe Barbara can help with this? Barbara Barbara commented 5 hours ago. Running it on shark would be an option. I will give it a try. Labels Edit Thomas commented about 4 hours ago. simulation Great idea. Good luck with that! Assign labels Barbara commented 20 minutes ago. Search labels Please make use of the new script. Utilize qsub to run it on the shark server. simulation qsub run_tool.sh You can fi nd more information here. Create new label Manage labels Barbara 20 minutes ago. Status changed to closed. Assigns the "simulation" label to the closed "Simulation is way to slow" issue. Barbara 76/141 GitLab as a Collaborative Working Environment
Milestones • Allow you to organize issues into a cohesive group and, optionally, to set a due date. • Milestones are usually created per-project. • You can create a milestone for several projects in the same group simultaneously. • On the group’s milestones page, you will be able to see the status of that milestone across all of the selected projects. 77/141 GitLab as a Collaborative Working Environment
Example: create milestone GitLab https://git.lumc.nl/CR/project-75-RNAseqHumanBrain/milestones/new New Milestone Title Complete simulation framework Description We should focus a bit on fi nishing the required simulations scripts and other related issues. Styling with Markdown and slash commands are supported Due date 2017-12-24 Create milestone Cancel Creates a new milestone to push things a bit :). Thomas 78/141 GitLab as a Collaborative Working Environment
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