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Put the --import-file back
Skyline needs the path to locate the LC-MS files not in the work dir. Removed by e960094
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  • MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline

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MSFragger-GUI/src/com/dmtavt/fragpipe/tools/skyline/Skyline.java

Lines changed: 2 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -255,11 +255,8 @@ private static void runSkyline(String skylinePath, Path wd, String skylineVersio
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writer.write("--full-scan-isolation-scheme=\"Results only\" ");
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}
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if (dataType.contentEquals("DIA") && overridePeakBounds) {
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// lc-ms file import is automatic when reading peptide list, but needs the DIA files imported separated for DIA SSL
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for (String s : lcmsFiles) {
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writer.write("--import-file=" + s + " ");
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}
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for (String s : lcmsFiles) {
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writer.write("--import-file=" + s + " ");
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}
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// todo: waiting for a fix (or clarification) from Brendan. Skyline does not allow this unless fasta has been imported

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