@sjcrh/proteinpaint-server 2.209.0 → 2.210.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dataset/termdb.test.js +2 -1
- package/package.json +5 -5
- package/routes/termdb.diffMeth.js +9 -1
- package/src/app.js +624 -518
- package/src/serverconfig.js +7 -0
package/src/serverconfig.js
CHANGED
|
@@ -50,6 +50,13 @@ if (!serverconfigfile) {
|
|
|
50
50
|
if (!serverconfig.port) serverconfig.port = process.env.PP_PORT || 3000
|
|
51
51
|
// default binary cmd paths
|
|
52
52
|
if (!serverconfig.tabix) serverconfig.tabix = 'tabix'
|
|
53
|
+
/* ships with tabix as part of htslib; used to write cached track files. Derived from an explicit
|
|
54
|
+
tabix path so a deployment with htslib off PATH does not have to set both, since forgetting the
|
|
55
|
+
second one only shows up the first time something writes a cached track. */
|
|
56
|
+
if (!serverconfig.bgzip)
|
|
57
|
+
serverconfig.bgzip = serverconfig.tabix.includes(path.sep)
|
|
58
|
+
? path.join(path.dirname(serverconfig.tabix), 'bgzip')
|
|
59
|
+
: 'bgzip'
|
|
53
60
|
if (!serverconfig.samtools) serverconfig.samtools = 'samtools'
|
|
54
61
|
if (!serverconfig.bcftools) serverconfig.bcftools = 'bcftools'
|
|
55
62
|
if (!serverconfig.hicstraw) serverconfig.hicstraw = 'straw'
|