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Internal page for MACH project members
Directories for data shared among members of project MACH
Internal page for MACH project members
Directories for data shared among members of project MACH
==== Directory organization for shared data ==== * /bio/db Public biological sequence and related data. * Data by project MACH will be kept under /data/mach/* is a person who put the data / did the analysis. * How MiSeq raw read data and analyzed data are organized will be desided among the users of the project.
==== Procedure to start the use ====
cd /data/mach
mkdir <user> (e.g. mkdir mickey)
==== Note about priviledges of users ====
Highest priority: Usage for MACH project by the project members.
===== List of users =====
|User |Family name |First name |Secondary groups |Note |
|bioadmin| | | |to install bioinformatic tools without using root by using su/sudo|
|joaquin|Rilling|Joaquin|fuse, machanal||
|so|Fujiyoshi|So|fuse, machanal||
|mickey|Kawai|Mikihiko|fuse, machanal||
|fumito|Maruyama|Fumito|machanal| |
|satoshi|Nagai|Satoshi|machanal| |
|kyoko|Yarimizu|Kyoko|machanal| |
|shoko|Ueki|Shoko|machanal| |
===== List of groups =====
|Date created |Group name |Purpose |Note|
|20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os|
|20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)||
|not yet|machdb| | |
|not yet|machweb| | |
|not yet|machmodel| | |
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
| | |
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |Size |
|/data/|775 (root-research)| |20TB|
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| |
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| |
* /data can be other path, for example, /home/proj
* <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |Last name |First name |
|mach|machanal|joaquin|Joaqui|Rilling|
|mach|machanal|so|So|Fujiyoshi|
|mach|machanal|mickey|Mikihiko|Kawai|
|ao|name_ao|kei|Kei|Yoshimura|
|ao|name_ao|fumiaki|Fumiaki|Morimoto|
|ao|name_ao|xiaojun|Xiaojun|name|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
|/bio/db| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
===== =====
===== =====
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |
|/data/|775 (root-research)| |
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project|
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project|
* /data can be other path, for example, /home/proj * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |
|mach|machanal|joaquin|
|mach|machanal|so|
|mach|machanal|mickey|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/db| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
==== Groups of priviledges ====
|Priority |Group name of priviledge |Purpose |Note | |
|High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)| |
|machcolab|Coollaborative studies by MACH members| | | |
|ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
|Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
===== Limitation of initial resources for default user account =====
|Queue name |Duration of one job |Memory per job | | |
|small|6hr| |medium|72hr|
|Group of priviledge |Number of simultaneous jobs | | | |
|default|e.g. 30?| | | |
Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu.
====== Internal page for MACH project members ======
====== ======
===== General note about data that are/will be managed by members of project MACH =====
Roughly speaking, three types of data will be kept, public biological sequence and related data, MiSeq data and Analized data.
* Public biological sequence and related data will be kept under /bio/db.
* Data by project MACH will be kept under /data/mach/<user>, where <user> is a person who did the analysis.
* How MiSeq raw read data and analyzed data are organized will be desided amont the users of the project.
==== Note about priviledges of users ====
Highest priority: Usage for MACH project by the project members.
===== List of users =====
|User |Family name |First name |Secondary groups |Note |
|bioadmin| | | |to install bioinformatic tools without using root by using su/sudo|
|joaquin|Rilling|Joaquin|fuse, machanal||
|so|Fujiyoshi|So|fuse, machanal||
|mickey|Kawai|Mikihiko|fuse, machanal||
|fumito|Maruyama|Fumito|machanal| |
|satoshi|Nagai|Satoshi|machanal| |
|kyoko|Yarimizu|Kyoko|machanal| |
|shoko|Ueki|Shoko|machanal| |
===== List of groups =====
|Date created |Group name |Purpose |Note|
|20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os|
|20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)||
|not yet|machdb| | |
|not yet|machweb| | |
|not yet|machmodel| | |
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
| | |
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |Size |
|/data/|775 (root-research)| |20TB|
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| |
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| |
* /data can be other path, for example, /home/proj
* <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |Last name |First name |
|mach|machanal|joaquin|Joaqui|Rilling|
|mach|machanal|so|So|Fujiyoshi|
|mach|machanal|mickey|Mikihiko|Kawai|
|ao|name_ao|kei|Kei|Yoshimura|
|ao|name_ao|fumiaki|Fumiaki|Morimoto|
|ao|name_ao|xiaojun|Xiaojun|name|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
|/bio/db| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
===== =====
===== =====
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |
|/data/|775 (root-research)| |
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project|
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project|
* /data can be other path, for example, /home/proj * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |
|mach|machanal|joaquin|
|mach|machanal|so|
|mach|machanal|mickey|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/db| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
==== Groups of priviledges ====
|Priority |Group name of priviledge |Purpose |Note | |
|High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)| |
|machcolab|Coollaborative studies by MACH members| | | |
|ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
|Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
===== Limitation of initial resources for default user account =====
| |Disk quote per user |
|default|500GB|
|Queue name |Duration of one job |Memory per job | | |
|small|6hr| |medium|72hr|
|Group of priviledge |Number of simultaneous jobs | | | |
|default|e.g. 30?| | | |
Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu.
MACH Meeting about soroban
==== Procedure to start the use ====
cd /data/mach
mkdir <user> (e.g. mkdir mickey)
==== Note about priviledges of users ====
Highest priority: Usage for MACH project by the project members.
===== List of users =====
|User |Family name |First name |Secondary groups |Note |
|bioadmin| | | |to install bioinformatic tools without using root by using su/sudo|
|joaquin|Rilling|Joaquin|fuse, machanal||
|so|Fujiyoshi|So|fuse, machanal||
|mickey|Kawai|Mikihiko|fuse, machanal||
|fumito|Maruyama|Fumito|machanal| |
|satoshi|Nagai|Satoshi|machanal| |
|kyoko|Yarimizu|Kyoko|machanal| |
|shoko|Ueki|Shoko|machanal| |
===== List of groups =====
|Date created |Group name |Purpose |Note|
|20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os|
|20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)||
|not yet|machdb| | |
|not yet|machweb| | |
|not yet|machmodel| | |
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
| | |
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |Size |
|/data/|775 (root-research)| |20TB|
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| |
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| |
* /data can be other path, for example, /home/proj
* <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |Last name |First name |
|mach|machanal|joaquin|Joaqui|Rilling|
|mach|machanal|so|So|Fujiyoshi|
|mach|machanal|mickey|Mikihiko|Kawai|
|ao|name_ao|kei|Kei|Yoshimura|
|ao|name_ao|fumiaki|Fumiaki|Morimoto|
|ao|name_ao|xiaojun|Xiaojun|name|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
|/bio/db| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers
https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
===== =====
===== =====
==== Assignment of users to a group ====
|Group |Assigned user|
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |
|/data/|775 (root-research)|
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project|
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project|
* /data can be other path, for example, /home/proj
* <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |
|mach|machanal|joaquin|
|mach|machanal|so|
|mach|machanal|mickey|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB |
|/bio/bin| | | |
|/bio/db| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers
https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
==== Groups of priviledges ====
|Priority |Group name of priviledge |Purpose |Note |
|High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)|
|machcolab|Coollaborative studies by MACH members| | | |
|ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
|Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)|
===== Limitation of initial resources for default user account =====
|Queue name |Duration of one job |Memory per job |
|small|6hr| |medium|72hr|
|Group of priviledge |Number of simultaneous jobs | | | |
|default|e.g. 30?| | |
Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu.
====== Internal page for MACH project members ======
====== ======
===== General note about data that are/will be managed by members of project MACH =====
Roughly speaking, three types of data will be kept, public biological sequence and related data, MiSeq data and Analized data.
* Public biological sequence and related data will be kept under /bio/db.
* Data by project MACH will be kept under /data/mach/<user>, where <user> is a person who did the analysis.
* How MiSeq raw read data and analyzed data are organized will be desided amont the users of the project.
==== Note about priviledges of users ====
Highest priority: Usage for MACH project by the project members.
===== List of users =====
|User |Family name |First name |Secondary groups |Note |
|bioadmin| | | |to install bioinformatic tools without using root by using su/sudo|
|joaquin|Rilling|Joaquin|fuse, machanal||
|so|Fujiyoshi|So|fuse, machanal||
|mickey|Kawai|Mikihiko|fuse, machanal||
|fumito|Maruyama|Fumito|machanal| |
|satoshi|Nagai|Satoshi|machanal| |
|kyoko|Yarimizu|Kyoko|machanal| |
|shoko|Ueki|Shoko|machanal| |
===== List of groups =====
|Date created |Group name |Purpose |Note|
|20191001?|fuse|To mount basemount for getting raw gigabase-order raw sequence files of Illumina MiSeq from Illumina's BaseSpace|probably set by default setting of os|
|20191001?|machanal|To share analyzed data among members of project MACH (e.g. at /data/mach/)||
|not yet|machdb| | |
|not yet|machweb| | |
|not yet|machmodel| | |
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
| | |
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |Size |
|/data/|775 (root-research)| |20TB|
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project| |
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project| |
* /data can be other path, for example, /home/proj
* <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |Last name |First name |
|mach|machanal|joaquin|Joaqui|Rilling|
|mach|machanal|so|So|Fujiyoshi|
|mach|machanal|mickey|Mikihiko|Kawai|
|ao|name_ao|kei|Kei|Yoshimura|
|ao|name_ao|fumiaki|Fumiaki|Morimoto|
|ao|name_ao|xiaojun|Xiaojun|name|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
|/bio/db| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
===== =====
===== =====
==== Assignment of users to a group ====
|Group |Assigned user |
|machanal|joaquin|
|machanal|so|
|machanal|mickey|
|machanal|fumito|
|machanal|satoshi|
|machanal|kyoko|
|machanal|shoko|
|fuse|joaquin|
|fuse|so|
|fuse|mickey|
===== Directory organization =====
==== For sharing data among project members ====
|Path |Permission |Purpose |
|/data/|775 (root-research)| |
|/data/<project>/|2770 (<project>-research)|To keep data shared among users of the project|
|/data/<project>/<user>/|2750|To keep data analyzed by the user of the project|
* /data can be other path, for example, /home/proj * <user> belongs to a group, of which name for the <project> may be simply the same as <project>, but can be different.
=== List of projects ===
|Project |Group |User |
|mach|machanal|joaquin|
|mach|machanal|so|
|mach|machanal|mickey|
===== For directories of tools and public databases of biological data =====
|Path |Permission |Purpose |Size |
|/bio|775 (bioadmin-bioadmin)| |25TB|
|/bio/bin| | | |
|/bio/db| | | |
|/bio/package| | | |
|/bio/package/<tool>/<version>| | | |
===== Queues / Groups of user priviledge (SLURM) =====
See belows for basic usage of SLURM at UFRO-CEMCC servers https://cemcc.ufro.cl/wiki/doku.php?id=slurm#useful_reference_pages
==== Groups of priviledges ====
|Priority |Group name of priviledge |Purpose |Note | |
|High|mach|Usage for MACH project by the project members.|Distribute evenly among users (e.g. for biological analysis and for simulation) (by ticket, nice value etc. on SLURM)| |
|machcolab|Coollaborative studies by MACH members| | | |
|ufro-internal||Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
|Low|external|Need to submit user form (e.g. Name, affiliation, purpose of usage, desired account if any)| | |
===== Limitation of initial resources for default user account =====
| |Disk quote per user |
|default|500GB|
|Queue name |Duration of one job |Memory per job | | |
|small|6hr| |medium|72hr|
|Group of priviledge |Number of simultaneous jobs** | | | |
| default | e.g. 30? |
Submit an application form if one wants to request large resources, say, storage, memory per queue, number of similutaneously running queues/cpu.