The fix is to change the line
ALTER TABLE `WebUploadTempFiles` ADD INDEX IF NOT EXISTS `repo_id` (`repo_id`);
to
ALTER TABLE `WebUploadTempFiles` ADD INDEX `repo_id` (`repo_id`);
in
seafile-server-10.0.1/upgrade/sql/10.0.0/mysql/seafile.sql
If it still fails, you need to remove that line. (because the index exists already then)