|
Size: 3031
Comment:
|
← Revision 15 as of 2023-04-25 11:27:50 ⇥
Size: 3748
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| <<Anchor(top|scroll to the top of the page)>> | |
| Line 2: | Line 3: |
| ---- | <<TableOfContents(2)>> |
| Line 6: | Line 7: |
| Several partitions are available share among all users with no quota per user. Every user is responsible of his data and should use the storage according to the good practices rules described here. | Several available partitions are shared among all users with no quota per user. Every user is responsible of his data and should use the storage according to the good practices rules described here. |
| Line 32: | Line 33: |
| __Open to users?__: Yes, but in specific folder only | __Open to users?__: Yes, in specific folder only |
| Line 45: | Line 46: |
| __Open to users?__: Yes, but in specific folder only | __Open to users?__: Yes, in specific folder only |
| Line 50: | Line 51: |
| * This folder contains home folders of all mib users. Each user manage their own home folder. | * This folder contains home folders of all mib users. Each user manages their own home folder. |
| Line 57: | Line 58: |
| __Open to users?__: Yes, but in specific folder only | __Open to users?__: Yes, in specific folder only |
| Line 74: | Line 75: |
| * Every user can make a folder and to work in. Users are responsible of removing their output folders when analyses are done. | * Every user can make a folder to work in. Users are responsible for removing their output folders when analyses are done. |
| Line 85: | Line 86: |
| * Most of bioinformatics software will be installed here. But please use the mechanism described in [[module]] to know how to load and use those programs. | * Most of bioinformatics software will be installed here. But please use the mechanism described in [[Submitting jobs]] to know how to load and use those programs. |
| Line 89: | Line 90: |
| {{{#!wiki green/solid === Not active yet === __backup?__: No |
|
| Line 90: | Line 94: |
| == Best practices == | __Open to users?__: Yes __Available on compute nodes?__: Local to compute nodes, each node has it's own scratch folder __Description__: * Automatically created }}} == Good practices == |
| Line 95: | Line 107: |
* Keep work folder clean * Keep home folder clean * Always have data in /seq * From /work to /projects == Quick links == 1. [[Computers description]] 2. [[Request an account]] 3. [[storage description]] 4. [[First login]] 5. [[Receiving sequencing data]] 6. [[transferring data]] 7. [[Submitting jobs]] 8. [[Monitor jobs]] 9. [[Install tools]] 10. [[Space management]] [[#top]] |
Storage description
Before using the current MIB infrastructure it is good practice to have some info about the storage available.
Several available partitions are shared among all users with no quota per user. Every user is responsible of his data and should use the storage according to the good practices rules described here.
Description Filesystems
The blue color for a box means that the filesystem (FS) is not available from the compute nodes.
The green color for a box means that the filesystem (FS) is accessible from the compute nodes.
Use the command df -h or lsblk /dev/sda to list filesystem and their size.
/seq
backup?: Not yet
Open to users?: No
Available on compute nodes?: No
Description:
- Raw sequencing files should be stored here.
- Only admins can write in this folder.
- Users can read all files present. If you receive new sequencing data contact the local admin to add it here.
/projects
backup?: Not yet
Open to users?: Yes, in specific folder only
Available on compute nodes?: No
Description:
- This folder will contain all users project file.
- Users can manage their own folders.
- All users can read all files
/homemib
backup?: Not yet
Open to users?: Yes, in specific folder only
Available on compute nodes?: Yes
Description:
- This folder contains home folders of all mib users. Each user manages their own home folder.
- Use your home folder to store files other than genomic data. Documents, scripts...
/home
backup?: Not yet
Open to users?: Yes, in specific folder only
Available on compute nodes?: No
Description:
- This folder contains home folders of all micevo users.
/work
backup?: No
Open to users?: Yes
Available on compute nodes?: Yes
Description:
- This folder should be used to run analyses. Input data may be read from a different filesystem but the output should always be in this partition.
- Every user can make a folder to work in. Users are responsible for removing their output folders when analyses are done.
/tools
backup?: No
Open to users?: Yes
Available on compute nodes?: Yes
Description:
Most of bioinformatics software will be installed here. But please use the mechanism described in Submitting jobs to know how to load and use those programs.
- Test data will also be available here. If you develop software or script please make small test data available here for all users.
- All users except guests and students have write permissions in all folders here. If you do create a folder in here please make sure to set writing rights to group.
Not active yet
backup?: No
Open to users?: Yes
Available on compute nodes?: Local to compute nodes, each node has it's own scratch folder
Description:
- Automatically created
Good practices
Coming soon
- Keep work folder clean
- Keep home folder clean
- Always have data in /seq
- From /work to /projects