-
Notifications
You must be signed in to change notification settings - Fork 11
/
Changes
103 lines (79 loc) · 2.61 KB
/
Changes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
v0.6.0 2021-07-14 Lyon
----------------------
core library:
- added ifelse and trywith constructs
- moved bio-stuff in new package bistro-bio
engine:
- precious items
- repo clipping
ppx:
- include script mechanism
bio:
- added Bedtools.merge
- added Samtools.faidx
- added SE_or_PE
- new wrapper rnaspades
- new wrapper busco
v0.5.0 2019-08-20 Lyon
----------------------
new design: 'a workflow evals to 'a
- workflows can now compute any (serializable) value besides paths
- list workflows can be spawned for parallel execution
- execution engine entirely rewritten, still allows exact incremental
garbage collection
- templates for bash script can now contain int and string variable
parts
- singularity support
- multinode execution engine
- HTML reports
- dynamic memory and processor requirements
- utils.Repo are best-effort rendered in case of errors
- many new modules in bioinfo
- ppx for templates with antiquotations
v0.4.0 2018-06-16 Lyon
----------------------
- ppx syntax extension to write workflow steps as regular OCaml functions
- new workflow type, that maps a command on all files of a directory in //
- use class types for phantom typing
- started a documentation!
- dry-run execution mode
- new docker files
v0.3.0 2017-06-21 Lyon
----------------------
- Compilation via jbuilder
- more docker images and wrappers
- various bug fixes
v0.2.0 2017-05-10 Lyon
----------------------
Major rewrite:
- new execution engine
+ generic notion of task graph (DAG)
+ compilation of workflow representation to a task DAG
+ logging facilities
+ transparent execution of commands through docker container
+ removal of intermediate targets during execution
+ notion of precious workflow (that should be kept no matter what)
- call of regular ocaml function as new type of workflow
- applicative term to express an action that should be performed after a
set of workflows has been successfully executed
- text logging
- logging as HTML report
- added a collection of Dockerfile scripts
- new bioinfomatics wrappers (many contributed by Sylvere Bastien)
and many bug fixes.
v0.1.0 2016-05-19 Lyon
----------------------
Many minor changes in API.
Installation scripts for tools are no longer considered part of
analysis workflow. Installing programs should be dealt with outside
bistro.
Features:
- heredoc for shell EDSL
- new np and mem tokens for scripts, as a way to use only the
resources that were allocated to a run
Bug fixes:
- bistro execution hangs on utop (f4f932f)
- don't save workflow in database statistics, just its id (issue #4)
v0.0.0 2016-01-21 Lyon
----------------------
First release on OPAM