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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.