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namespace:doc-mach:soroban [2020/05/19 02:34] (current) mickey |
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| ====== Internal page for MACH project members ====== | ====== Internal page for MACH project members ====== | ||
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| ===== Directories for data shared among members of project MACH ===== | ===== Directories for data shared among members of project MACH ===== | ||
| - | ====== Internal page for MACH project members ====== | + | ==== Directory organization for shared data ==== |
| - | ====== ====== | + | * /bio/db |
| + | * Public biological sequence and related data. | ||
| + | * /data/mach/<user> | ||
| + | * Data by project MACH will be kept under | ||
| + | * <user> 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. | ||
| - | [[:namespace:doc-mach:installed-software|List of software installed on soroban]] | ||
| - | [[:namespace:doc-mach:usage-soroban|Usage of 'soroban' server for non-MACH users]] | + | ==== Procedure to use /data/mach/<user> ==== |
| - | ===== Directories for data shared among members of project MACH ===== | + | <code> |
| + | cd /data/mach | ||
| + | mkdir <user> #e.g. mkdir mickey | ||
| + | </code> | ||
| - | ==== 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. | + | ==== 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| | ||
| - | [[:namespace:doc-mach:meeting|MACH Meeting about soroban]] | + | |**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. | ||
| \\ | \\ | ||
| + | |||
| + | |||