Differences

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--- namespace:doc-mach:soroban [2019/12/12 15:54]
mickey [About MACH UFRO server 'soroban']
+++ namespace:doc-mach:soroban [2020/05/19 02:34] (current)
mickey
@@ Line 5: / Line 5: @@
 ======   ======
+[[:namespace:doc-mach:installed-software|List of software installed on soroban]]
-===== General note about data that are/will be managed by members of project MACH =====
+[[:namespace:doc-mach:usage-soroban|Usage of 'soroban' server for non-MACH users]]
-Roughly speaking, three types of data will be kept, public biological sequence and related data, MiSeq data and Analized data.
+===== Directories for data shared among members of project MACH =====
-  * Public biological sequence and related data will be kept under /bio/db.
+==== Directory organization for shared data ====
-  * 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 ====
+  * /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.
-Highest priority: Usage for MACH project by the project members.
-===== List of users =====
+==== Procedure to use /data/mach/<user> ====
-|**User** |**Family name** |**First name** |**Secondary groups** |**Note** |
+<code>
-|bioadmin| | | |to install bioinformatic tools without using root by using su/sudo|
+cd /data/mach
-|joaquin|Rilling|Joaquin|fuse, machanal||
+mkdir <user> #e.g. mkdir mickey
-|so|Fujiyoshi|So|fuse, machanal||
+</code>
-|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 ====
@@ Line 157: / Line 49: @@
-====== Bioinfomatic software ======
-Tool1
-## Protocol\\
-# Types of download\\
-# Types of decompress\\
-# Types of install\\
-# Types of version check
-## _template\\
-## anvi'o\\
-## ARAGORN\\
-## ARB\\
-## ascp (aspera connect)\\
-## bamtools
-test after raphael modified permission of group on 2019.06.05