Bashing irreproducibility with shournal
Abstract Arguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-53811-9 |
| _version_ | 1827327867116060672 |
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| author | Tycho Kirchner Konstantin Riege Steve Hoffmann |
| author_facet | Tycho Kirchner Konstantin Riege Steve Hoffmann |
| author_sort | Tycho Kirchner |
| collection | DOAJ |
| description | Abstract Arguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the shell or suffer from a large overhead. Here, we present shournal, which integrates tightly into the shell and automatically records all shell commands along with their associated file events. Thus, for all files, it can later be told how they were generated and processed. Additionally, it allows the creation of detailed reports for whole project folders. shournal retrieves its data directly from the Linux kernel and allows the monitoring of whole process trees with low overhead. |
| first_indexed | 2024-03-07T15:08:39Z |
| format | Article |
| id | doaj.art-e19d9cd0d27442e6b1bd452fb83cef2a |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-07T15:08:39Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-e19d9cd0d27442e6b1bd452fb83cef2a2024-03-05T18:49:04ZengNature PortfolioScientific Reports2045-23222024-02-011411710.1038/s41598-024-53811-9Bashing irreproducibility with shournalTycho Kirchner0Konstantin Riege1Steve Hoffmann2Computational Biology Group, Leibniz Institute on Aging — Fritz Lipmann Institute (FLI)Computational Biology Group, Leibniz Institute on Aging — Fritz Lipmann Institute (FLI)Computational Biology Group, Leibniz Institute on Aging — Fritz Lipmann Institute (FLI)Abstract Arguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the shell or suffer from a large overhead. Here, we present shournal, which integrates tightly into the shell and automatically records all shell commands along with their associated file events. Thus, for all files, it can later be told how they were generated and processed. Additionally, it allows the creation of detailed reports for whole project folders. shournal retrieves its data directly from the Linux kernel and allows the monitoring of whole process trees with low overhead.https://doi.org/10.1038/s41598-024-53811-9 |
| spellingShingle | Tycho Kirchner Konstantin Riege Steve Hoffmann Bashing irreproducibility with shournal Scientific Reports |
| title | Bashing irreproducibility with shournal |
| title_full | Bashing irreproducibility with shournal |
| title_fullStr | Bashing irreproducibility with shournal |
| title_full_unstemmed | Bashing irreproducibility with shournal |
| title_short | Bashing irreproducibility with shournal |
| title_sort | bashing irreproducibility with shournal |
| url | https://doi.org/10.1038/s41598-024-53811-9 |
| work_keys_str_mv | AT tychokirchner bashingirreproducibilitywithshournal AT konstantinriege bashingirreproducibilitywithshournal AT stevehoffmann bashingirreproducibilitywithshournal |